Dear MMG,
GPS Controller is only meant for diagnostics. You can theoretically run it in tandem with NMEA Applications like ArcPad, but I would not recommend this. You will get frustrated and max out the program memory on the Juno very fast.
To get the best performance out of ArcPad 7.1, you will need to purchase Trimble GPS Correct. It will allow you to create post-processable sessions in ArcPad, and allow you to take advantage of real-time corrections.
However, if you do not plan to post process in ArcPad, and you will not be utilizing VRS, or real-time base station corrections, you can just run ArcPad by itself in NMEA and it will gain WAAS corrections. WAAS correction require line of site to the sout (also depends on where you are located geographically), however you will celebrate sub-meter accuracy with WAAS on the Geo2008 in real-time.