They can be a little difficult to line sometimes, you may want to try first just putting the pipes up to see if they line well. One of them may be slightly bent too. I've seen it, but a reasonably easy fix.
I used to put a block of wood under the muffler or pipes with some shims and tried to get them as close as possible to where they should be. It saves a lot of contorsions for lining/tightening.
If they seem to line up good,then just don't tighten one fully and then go on to the other one, you should alternate between them as you tighten. A little wiggling also helps as you tighten them up.
Loosening the cross pipe can help too.
And look in the holes too first, there may be carbon/crud/nicks in there that may need to be cleaned up first.
For years I never had the OEM gasket(s) at the muffler, brass shim stock worked just fine, a small piece of scotch tape so it does not unravel,stick the muffler over it...that's it!