and also if we book in the last minute, seats will be there as we are travelling during peak season ?

You do not book anything in Switzerland. Tickets can never sell out.

On the day you choose which train you'd like to take and add it to the app before you board. Then you enter the train and sit wherever you want. You do not "book" anything, the Eurail pass is your ticket.

Use SBB app or sbb.ch to get an idea of all the connections.

1. Lucerne - Engelberg + walk to the cable car. Buy tickets there.

2. Lucerne - Interlaken Ost train and then either via Lauterbrunnen or Grindelwald. Book tickets from Interlaken Ost through jungfrau.ch or at Interlaken train station (same price).

3. Weggis does not have at train station. Bus to Küssnacht am Rigi (not included) and then train or boat to Lucerne (50% discount)

4. Cable car Weggis - Rigi and back Rigi - Vitznau cogwheel railway or the other way around (50% discount). Vitznau - Weggis : bus (not included) or boat (50% discount)

5. Lucerne - Brienz train and then boat. Everything is included, you only add the train and the boat to the app before boarding

Again please use the SBB app and Google Maps to find the nearest stop from your hotel

Thank you @thibcabe 

can you explain 3rd and 4th points ? 
so for these journeys I need to take mountain trains ?

Yes obviously as you are going to the top of the mountains

3. Bus to Küssnacht (full fare ticket) and then train to Lucerne (included) OR boat to Lucerne (50% discount). Then train to Alpnachstad (included) and mountain railway to Pilatus (50% discount)

4. You get a 50% discount for the cable car and/or mountain railways (2 ways to get to the top)

What did you mean by train to Lucerne?

you meant return journey from Mt Pilatus ?

Your journey will look like this :

- Weggis - Lucerne - Alpnachstad - Pilatus OR Weggis - Küssnacht - Lucerne - Alpnachstad - Pilatus