The rail planner app is very incomplete for Spain because RENFE (Spanish railways) don't share their complete timetables with the rest of the world. In general, the rail planner app should not be used to plan, since it does not get enough updates to be reliable. In addition, it is not complete for some countries (Spain, Italy) and some other countries are missing entirely (also see the "About the timetable” link on the planner's start screen).

The best is to use national planners (e.g. RENFE for Spain and CP for Portugal) and for international planning, the German railways planner is a good choice, although they will be incomplete for the same countries as the rail planner app. For routes between Spain and Portugal, also check seat61 (which has good advice on many more routes too).

Unfortunately, RENFE are generally not really customer-friendly. They've stopped the night trains between Spain and Portugal and they’ve made booking reservations for their trains cumbersome.

As above.

For your first trip-skip it by train (NOT direct at all) and use a bus=direct.

Shorter trips In ESpana that would cost less as 1 travelday are much better done by direct online booking. IF yoiu intend to make more trips IN ES, then (assuming you are junior?) also consider buying the Tarjeta Joven=jnr discount card for just 6€ and get 25-40% discounts. Can buy on the spot in any counter-no foto needed, just ID

For travel In PT on CP there is (was?) also a youth pass including stays at PT YH=hostels.

Thank you, all advice is appreciated. We are seniors, never been to Europe,  so this is really an adventure for us. Have been to the German rail site and they don’t show any trains (Lisbon to Madrid) trains either. I was looking at the  eurail map and it appeared to show a direct line between Lisbon and Madrid, guess I can’t rely on that map to show the most direct lines. I guess this planning won’t be as easy as I originally thought. 
 

I should mention that this trip begins in November 2022. 
Since I’m so new this, can I ask if anyone has suggestions on which station (I’ve noticed that several  city’s have multiple train stations) to use for the best short term sightseeing base. I know we will be missing a lot of wonderful sights by only spending a day or two in each location but this is a transition trip between Porto Portugal, to Budapest where we will be getting on a river cruise. 
 

city’s with multiple stations that we would like to spend a day or two exploring before moving on.

Madrid

Nice (assuming this is where we can see Monaco)

Venice

also please tell me if I’m crazy
Rob 

German railways will also be very incomplete for Spain, since the ever so “customer friendly” Spanish railways don't send their timetables (or only very few of them) to the rest of the world.

www.thetrainline.com is one of the very few sites that does seem to know Spanish timetables. Do take into account that in Spain, Ouigo and Avlo trains cannot be used with Eurail.

Also, if your trip is in November, that is too far ahead for French, Italian and Spanish railways because they haven't finalised and published their timetables yet. However, you can make a planning by using dates before 12 June (that's the start of the summer timetable) on the same day of the week. The come back in September to verify planning. Most timetables won't change much but there will be some small changes here and there.

Note that there is currently no direct service Mardrid - Lisbon as RENFE (spanishrail) stoppedal their Nighttrain services (was the last direct train) 
Currently you have just few connections with a change near the border of spain/Portugal 
depending on your route you may take the bordercrossing train in North of portugal Porto - Vigo  and travel from there onwards. 

as already mentioned by @rvdborgt itś to early to make the final shedule as there are till then some timetable changes. You can start researching know to have a rough plan and confirm then your shedule 2-3months in advance of your trip as maybe small changes in the timetable will happen :)  Please note that in Spain you have to pay ontop of eurail for each train for reservations usually 15€ per person as spain made almost all their trains reservation compulsory :/

Fees in Spain depend on class and train type. See this page (scroll down to Spain), often 4, 6.50 or 10 EUR, although in 1st class it can also be more expensive.

Listen to what user ‘rvdborgt’ says, I would suggest! He seems very knowledgeable and provides useful links for verification.

As for your question about multiple train stations, in most major European cities all the train stations are quite close to the city centre. Certainly not more than a mile (or absolute max two miles) out. Remember that the reason there are multiple stations is that in the 1850-1900 period there were multiple competing train companies which all built their own stations… but they still wanted them in the city centre! And of course the cities at that time were usually smaller than today - so stations which might have been on the edge of the city centre in 1850 would be pretty much bang in the centre today! So you don’t need to worry about basing yourself around any particular station to see the sights… Just jump on a bus or Metro if you need to take short journeys - or take a taxi… or walk, and enjoy the city atmosphere...

It seems that the Spanish railway system/reservations/timetables is really not very user-friendly at all, in fact it’s gone backwards in the last couple of years. But there is a (very slow… but maybe you’re not in a hurry?) train route from Lisbon to Madrid - you can find it on https://www.bahn.com/en. Looks like the 2 legs in Portugal don’t need a reservation at all but the two legs in Spain will need a reservation each...

The only thing I would add is that Venice is one of those very few cities where the ‘other’ train station (Mestre) is a long way from the city, it’s 5 miles away on the mainland. The train station in Venice itself is Santa Lucia. But a lot of tourists find that accommodation on the mainland is much less expensive, so stay there and just ‘commute’ the 5 miles and back by train, each day they visit Venice itself.

So in summary, if you want to go Lisbon - Madrid - Barcelona with a Eurail pass:​​​​​​​

Using 1 day of your pass travelling Lisbon - Madrid: 3 trains, just jump on the train at Lisbon Santa Apolonia Station (no reservation), change at Entroncamento (no reservation), change at Badajoz with a couple of hours’ wait until the 16:45 train to Madrid (which runs every day except Saturday) - this will allow you time to make your Spanish reservation at the Badajoz station ticket office before the train departs.

You should even be able to make your onward reservations for your high-speed train from Madrid to Barcelona for a later date, in the ticket office in Badajoz. Alternatively you can make them at any station’s ticket office in Madrid after you arrive.

I hope this is useful. Happy travels!

PS the above is my understanding, I recommend doing your own research of course!