Having one in the shallow end on the skimmer side and one in the deep end ~opposite the skimmer would be optimal for your set up. However having the one opposite the skimmer and the one in the shallow end be on the shallow end wall ~ 3' out from the side opposite the skimmer would also work well. What you are trying to do is get the water to move in a 'circular' motion around the whole pool so that any floating debris gets to the skimmer for removal before it can sink and require the vacuum to remove. If the skimmer had been in the center of the pool, you could have put both returns on the skimmer side wall, one at each end and the flow pattern would have had the water being forced to the center and into the skimmer - having the 2 returns on the opposite wall defeats this flow pattern because it will direct the debris to the center of the pool on the other side than the skimmer

The hayward 1408 inlet/ outlet fittings don't have to be 100% flush against the wall - the flange is behind the liner and the faceplate against it is what seals the liner - but it's best to have them ~ flush to the wall (the 1408s work on kidney pools so if the radius of the bowed wall you are working with is less than 6', all is fine).

I'm here almost every day if you need to bounce any ideas or questions off me. Good luck with the project!!