kd, welcome to the forum! As you are removing the water from behind the liner, use your wall brush to remove the wrinkles that will form, try to work them parallel to the wrinkle from both sides, if one gets tough, kill the removal pump for a few minutes while you work on it.
As for getting the liner back into it's track, pour hot water on the entire area (hot water from your tap should be enough) then work it in from both sides. (I could probably get it in w/o the hot water but there's no way I can describe the 'technique' in a post ) If you are still having problems after trying the hot water thing, personal message me and we'll work out a way to talk 1 on 1, so I can help you further. Good luck with the pool, and enjoy it while the weather's good!! -Waste