I've found with using guncon's (not aimtrak's, but I'm sure they are the same in MAME) that getting the software to see just one axis is very difficult. Given enough tries, it is possible to set up a pair of guns inside MAME and just play, but it takes a LONG time, IMO. I've found the best thing to do is just get a setting in each field that I want setup and then edit the cfg file to get it correct.
Also, I only set up gun games in the default.cfg file. If you want, I suppose you could do it for each game one at a time, but you will be adding the same config to a series of games for no reason. If you just have the trigger button as button 1 and then set up your standard button 1 (from the CP) immediately afterward (or before), you will set MAME to respond to one or the other. Repeat for each gun button and you should be golden!