Tracking sites use FAA data for the most part, augmented by ADS-B data nowadays.
For FAA data, they use what's in the National system. This is usually 99%+ of IFR flight plans, and some VFR flight following flight plans. IFR flights plans that aren't included are those that are local area pop-up requests(staying with the same approach control with a pop-up IFR clearance).
For VFR flights, the only data in the NAS is what's input by controllers for flight following that leaves their airspace(leaving a TRACON headed to a center or another facility, usually; sometimes you can get a NAS code for just a local flight). VFR flight plans sent to and activated by flight service are not sent to ATC, all they are is a tool for rescuers to search for you if you're late and never check in and a search needs to go find you.