If you look a bit down in this manual you can see how to make a booking through the Austrian Railways website. 

The trains from Vienna to Bratislava are regionaltrains and cant be reserved. There 2 trains per hour one to Bratislava hl.st (Mainstation) and one to Bratislava Petrzelka (south east Bratislava) 

You can only reserve the IC and RJ connection going to Bratislava Petrzalka which is a bit far from the center.
For the hourly direct Regio Express trains to Bratislava hlavna stanica (main station) you can’t make a reservation. Just board a train and get a seat. You will definitely find one, no worries.

@AnnaB except one IC in the afternoon  and one Railjet in the evening all trains between Vienna  & Bratislava are regionaltrains and cant be reserved. 

Okay, so these aren’t super busy and I should be able to find a couple seats ?

Yeah, except in extraordinary cases you should always be able to find some seats if you are not a group of 20 people .

Canuck: maybe you should realize these trains are just as the GO_ontario: there is NO controlled access and thus they cannot deny boarding. You stand if you really cannot find seats and are too shy to ask someone to remove his overdose of luggage from the seat beside-this is also common pratcice.

There is heavy commuter traffic between the 2 thus peak hr trains can be quite full with workers going home (wages in AT double those of SK-heritage from the old past)

In case you really cannot stand it-htere are also BUSes ev 30 mins between the 2=via airport-and a single is just 5-6€. These bring you tioll right smack in the centre.

IF you happen to be >62: you can get a customer card (bring foto) for free local train travel INside SK at the special clients helpdesk i main station.

@seewulf  okay so I currently have reservations for Muenchen HBF —>  Wien HBF train 63. On my ticket for the travel day I have Muenchen HBF —> Bratislava h.l. st. with a 46 minute change at Wien HBF, where there is a train at 14:16 to Bratislava. 

I will just show the same ticket for both trains on this journey, the reserved and the unreserved as it is only 1 travel day correct? (It shows Muenchen HBF —> Bratislava hl.st. so I presume, I’m just confirming) and what you are saying is there is no way for me to reserve that second portion Wien hbf at 14:16 to Bratislava correct ? Even on the Austrian rails site?

ps. I guess if there is no seats I can always stand or continue every hour waiting for one with some XD

Also, I do see a train 14:42 direct Wien HBF to Bratislava hl st which require reservation. Perhaps I can book that one on the Austrian rails site if I really want one ? Not sure if it would work maybe you would know ? @seewulf 

The 14:42 has optional reservations, just like the Munich - Vienna train.

But trust us, you don't need a reservation for a train mid-day Vienna - Bratislava. Just take the 14:16 one, you'll be fine.