If you choose to go the clear stamp route, make sure that the set you buy is designed specifically for ease of lining up. (My first alpha sets were not, and I don't use them even though I like the font.) The backing of the stamp needs to be square along the bottom as do the sides so they line up properly, and the backing needs to be just the right size for the letter- not bigger on one side than another, etc. The description of some currently available alpha sets, like those at Clear & Simple Stamps
, state they are designed to easily line up.
I line up my clear photopolymer stamps face down, let them rest/relax a moment to control stretch that may have occurred as I pulled them off the backing sheet, then put a grid-lined acrylic block over the back, press along the block to insure adhesion, and lift- they should be aligned properly. (If they fall off you may need to rinse them to restore their natural stick.) This method really helps if any of your stamps are long and skinny- prevents stretch that might occur if you attach them individually to your block by hand. If a letter is needed more than once, I move it from the first spot and place in the second, then add the next letters, etc., and stamp. I then go back and stamp individual repeated letters that were missing.
Another thing to consider when stamping individual letters is the spacing between, called kerning. It is more pleasing to the eye when the spacing between letters is proportional and some letters sort of tuck up next to others. A capital 'W' and 'A' next to each other are good examples of a need for kerning- see the examples at wikipedia.org. For this reason I was unhappy with wood block letters being arranged side-by-side to stamp as one- no kerning. It's also the reason I usually prefer to stamp letters individually with clear stamps along a light pencil line, so that I can control the spacing. Often, instead of a pencil line, I use a post-it to make my line and prevent smudges, but post-its don't work if any letters have an extender going below the line.