If you can afford it now, I'd suggest upgrading your stock speakers too. A sub won't necessarily overpower your stock speakers, but it depends on what size and power rating you choose for your sub. One 10", 12", 15" ? Also, seeing as you still have your stock speakers, do you still have your stock HU? If so, make sure your stock HU has some RCA preouts to actually run any sub you buy.

You can always adjust how much bass the sub is putting out, by some HU's and by the amp, so you should be able to find some sort of balance between bass and your mids and highs from your stock speakers.