I think it depends on the type of system you bought. If, for example, you bought an Onkyo or Yamaha HTIB, which usually contain a decent receiver, you could probably swap out subs and speakers, and in fact this is the most common upgrade mentioned by forum members.
If, however, you bought one of the HTIB's that has a combined DVD player/sound processor/amplifier, well, those "all-in-one" systems sometimes use dedicated connectors that would not allow you to be able to swap speakers around, perhaps including subs.
There are 2 types of subs, those whose power comes from the receiver's amplifier and those with a built in amplifier. The "powered" subs, who contain their own built in amplifier, are usually connected by a single RCA cable, and it's likely that you might be able to swap subs around if your "all-in-one" system has a separate RCA "Sub out" jack. Otherwise, I doubt that you'll be able to do much swapping.