Must get both
We just did a major avionics upgrade to our Beechjet. If you get the GMX-200, you must also get a GPS-400 or similar GPS and the GDL 69 to go along with it. It will not couple to the ship's FMS for anything. It is a complete stand alone unit. It is a very good SA tool with the plates and weather on there. If you want a picture of what it looks like installed, PM me and I will email you one.
As far as WAAS goes. We upgraded our GPS's to the 4000S vs. the 4000A's that are on most Beechjets (except for the newer ones). The 4000S's are WAAS capable, but the AMS-5000 has not been approved by the feds to do LPV minimums yet. I am told the target date for that is in spring 2008 sometime. It will be a $10k software upgrade if you have the 4000S's installed already. I can say that the 4000S's are spot on for accuracy. The error in flight has always been "0.00 nm" on every flight since the install, and the error probability has been no worse than "0.01." I have fed approval for operations in B-RNAV, P-RNAV, RNP-10, and MNPS/NAT (not that I would ever need it for the Beechjet).