When you listen to a set in the store they will sound different in your car. If it is a box, then see if there is anyway you can have them run wires to your car with the box in it to listen to it. Just for the sub of course. Definitely listen to the speakers first and find out what is driving the speakers on the rack. If the shop has amps driving the speakers you are listening to, then you put them in your car hooked up to the stereo without an amp and wonder why they don't sound as loud, then you know it is because of the amp. Different amps perform differently as well. For instance, IMO - Kenwood sucks as a subwoofer amp. It may say it is a 100W amp, but I think the Kenwoods lack current which is more important for good, deep accurate bass. Find a set of subs that you like. JL audio makes some real nice subs like Tarheel said. IMO, don't get anything bigger than 12" because then you loose accuracy and it will be muddy in the higher bass notes. Once you find that set of subs, test the amps with the sub you want to get. You will find some amps will push them really well and some may not. It depends on what sound you want out of them. You may find that a cheaper amp pushes them really well and better than some name brand more expensive ones. The amp is crucial to the quality of the sound. A super cheapo amp will make the best subs sound like sh!t and a quality amp will make cheapo subs sound better than high quality subs. The cheapo subs just won't last long.
I am rambling so I will stop now.