Best way to do it is install everything on the bike and make sure your chain adjustment is set at the lose end so you have full adjustment when it does stretch. Then just put the chain on and mark the chain where it needs to be. It's best to put the bike in gear and pull the chain tight then mark it. Make sure you take out an even number of links but I'm sure you knew that.
On a side note: If you don't have a chain breaker you can use a grinder, dremel, or any other method of grinding tool. Just grind off both rivet heads on the link you need to remove. Once the rivets are ground down put the chain in a vice with the ground rivet side up and crank it tight but not too tight that it distorts the chain. Use a hammer and screwdriver or cold chisel and pry the plate off that link you ground down. Try not to lose the rubber o-rings as they come in handy if you need them in the future.
Also when installing the master link after you get your chain at the correct length you can make it easier with a set of pliers (channel locks preferably) Put the link through the chain, hold the side plate on with your fingers and put a nut over one of the rivet holes and squeeze the plate on with the pliers. working from one rivet to the other until you can see the groove for the lock plate. Then push the lock plate on using the same pliers. Make note with the lock plate though. It will go on in either direction but should only be installed one way. The rounded side should be the front and the open end should be in back. Direction of chain movement going forward <-- link lock should be installed like this
http://www.your-adrenaline-fix.com/image-files/master-link.jpg
