I want to add a second garmin unit to my collection. Base camp recognizes my unit in the device positon, but will not record it in the top window.

A better way to ask this question is, will Base Camp work with more than one connected device data?

Yes it will, I often have multiple devices connected. If it shows in the bottom left hand pane then I'm not clear what your issue is?

I have a Zumo 660 that displays in the bottom paine (devices) and loads into the top pain (my collection) when connected that remains in (my collection) when disconnected so I can acces and edit the data. All of the waypoints displaythe selected graphics.

Now when I connect my OTR-700, it only shows up in the bottom paine (devices) and all of the waypoints display a blue flag and will not display in the top paine ( my collection).

Leads me to think that the OTR-700 is not compatible with base camp?

Won't display anyway by default.  If you want the data in the top pane you need to copy it there.

Thanks, I will try that in a bit. When I connected my first unit Zumo-660 it went automatically.

It wouldn't have, that's not how BaseCamp works.