My wife and I will be taking the afternoon IC train from Faro to Lisbon. Is there a better side to be located for scenery along the trip and is there a way to determine the window location of seats to avoid being in the middle of two windows?

Are you traveling first class or second class.
First class seats are 2 aisle 1, second class are 2 aisle 2.

These photos from my trip report show the seats ( 1x2 and 2x2).
https://cimg9.ibsrv.net/gimg/www.fod...dc848f0af1.jpg

https://cimg8.ibsrv.net/gimg/www.fod...4718e43fd4.jpg

From what I remember the windows are shared between 2 rows of seats but don't remember if any are blocked.

We book the seats depending on the location of the sun ( having the sun shining on our eyes is not pleasant).

Between Lisbon and Porto I prefer the west side of the train but between Lisbon and Faro didn't really matter .

Thankyou. We will be travelling 2nd class. I can get a good feel for the window locations from your photo. Will stay on the RHS to avoid the afternoon sun.