Two links short is not uncommon.
From Good Ol' Sheldon Brown:
The best technique for setting chain length is to thread the chain onto the large/large combination, without running it through the rear derailer. Mesh the two ends on to the large chainwheel so that they could be connected (outer link meets inner link), then make the chain one complete link (one inch) longer than that. In almost all cases, this will give the optimum length.
The joiner link you're referring to is actually a master link, and no, don't add more master links. It will weaken the chain more than a master link already does. I am NOT a fan of chains with master links.
If you want to do it yourself, you'll have to get a chain tool, like this one,
http://www.parktool.com/products/detail.asp?cat=5&item=CT-7 ,then watch this video
http://bikeride.com/chain-tool/
and either go back to the shop and get them to give you 2 more links, or buy another of the same chain, and use links off of that one. I would buy another chain, so you have LOTS of extra links.
Or if you don't want to do it yourself, go back to the shop and tell them you want two more links added. And don't let them charge you for it. You paid for every link they kept after shortening it, so you still own the links they kept. They SHOULD have given you the rest of the chain for this exact reason.