If I'm reading this righ, it sounds like your liner was offset to begin with, you might be able to shift it (even with the return and skimmer connected in).

You would take your large overlap end as your starting point, letting a little more liner down into the pool, (you'll only be able to do this with little to no water in it) then pulling that slack towards the center, then work it towards the other side, up and over until you're realtively satisfied that you have enough overlap. work anything else that's bunched towards the opposite end of the skimmer/return area. Your return and skimmer may give you a problem but if you do it an inch at a time it may work enough for you to hold up
If you stick a shopvac behind the liner you should get a good idea of what it will do when it's full/filling since the shopvac pulls it towards the walls - if there's still a lot of space (3" or so) that needs to be filled between liner and wall, it should be fixed/adjusted before adding water or else the same will happen again.