My 98 tsi came with a cd charger! Same as a gst so I'd imagine yours did to!

Did it also have an amp under the passenger seat?

cd changers and amps were optional equipment

Would the plugs only be there if those were ordered?

It depends on what stereo system it was optioned with. It would have a double din infinity deck. Amp would be under the pass seat and 10 disc cd changer would be in the right rear of the trunk area. 97-99 is a 10 disc changer and 95-96 are a 6 disc.

If you remove your passenger's rear tail light access cover and peer down in, you may find the pre-wired DIN plug.

Initially I wanted to keep my stock stereo and find a way to integrate an AUX-input through the CD changer. Unfortunately, I got in over my head when I found that a clock signal is required to activate the stock units CD changer input. Eventually I caved and went aftermarket, however NOW I've found a guy who does a lot of stock-stereo Aux-input modification. If you are interested in staying stock but having an Aux input, check him out:

Factory Radio Service, Car Factory Radio Services

The car didnt have a stereo installed when i bought it. But after tracing wires i noticed an xm radio box under the passenger seat. There are other plugs that were wrapped with electrical tape. I will go look in the trunk to see if i see anything.

Yes and a amp under the seat, not sure about the disc changed ill have to check. My 95 has all the wires for a amp and disc changer but when I got it no amp under the seat and had a aftermarket head unit.