5.25" sub size, but some have mdified it to except a 6.5". Yes, if they didn't "wire" it up right a aftermarket headunit will disable the factory sub. In all actuallity the factory sub isn't all that great along with the amp that pushes it not being all that great either. If I remember correctly the amp uses a integrated IC for amplification, which is just about the lowest quality you can get and not much "real" power unless you go with a really big one like is used from time to time in cheaper amplifiers like Pyramid. I think it only put out something like 20 watts, which isn't much for powering a replacement. Since you have an aftermarket unit, you'd be better off getting a littel 100 watt amp and upgrading the sub in the factory enclosure to a 6.5".
[This message has been edited by Khw (edited 11-01-2013).]