If your subs are wired directly from the head unit with RCA's, then they shouldn't have touched anything to so with the subs unless they were adding in another amp and splitting the signal. Did you check your head unit settings to see if the messed with the sub output on there. Most car audio places will turn the sub level down on there so they can hear the other speakers better and also so they don't mess up your amp settings. Try looking on there first and if not then looks like you will have to rip your car apart and figure out exactly how they hooked up the new speakers.
