An easy method to align a two layer PCB
Not easy, but I use an involved method that uses "alignment pins" to get perfect alignment every time.  This works very well with the toner transfer and photo paper method and might work for press and peel as well.


Dot the edges of your layout with evenly spaced pads used for alignment holes. 3 - 4 per side is sufficient.  You may need to distribute more into the center as well if the board is largish.  Use really small drill holes in the pads, so that you can accurately find the center.  
Print the two sides to your transfer paper and make an additional copy with just the alignment holes.  
Transfer the alignment holes to your board and use this as a guide to drill holes.  As an alternative, you could tape a normal paper copy of the holes to the board and use that as the guide.  But, I think it's more accurate to actually transfer it.  The size of holes should just small enough to pass pins or component leads through.  I like to use 18mil bits and use clipped off resistor leads as the alignment pins that I collect from previous projects.  
After drilling, remove the toner by sanding or acetone.  You should be left with the bare copper again and drilled holes.
Drill out the two transfer paper layout sides with the same bit.  Note, I hand drill both the board and transfer paper holes, so that they are perfectly centered.  This can be tedious especially if you use thick boards.
Trim down the two transfer paper layouts sides, so that they are slightly smaller than the board.  This is important because you need to tape them down after the alignment procedure.  
Align the two transfers over each side of the board, so that you can pass the alignment pins straight through the set of holes.  Then adjust each pin, so that they are all more or less perpendicular.  This should make everything aligned.  Carefully, tape down both transfer sides to the board securely and finally remove the pins.