TC 6.1.0 needs to be checked in correctly. It does have a nap file but it needs the 3.0 catalog.z file. If you have a subscription with nai then you can download the TC again. In the new download you will find the catalog.z file. Extract everything in the zip file to a temp directory.
Follow the check in procedure (not the add nap procedure) for new software, click yes to overriding the existing TC items.
If you still don't see it in the Deployment task then you should use the remove package feature to remove it.
Then manually navigate the directory structure on the ePO server and delete the directory that contains the TC software. Then go through the check in procedure again.
Once TC is installed correctly in the ePO database deployment and managment of the product becomes as easy as it was in 2.x, except that removal and installation have changed to a deployment task.
One note of caution though. Network Associates discourages the use of Thin Client. I kept getting told this, after a year and a half of hearing it a tech finally told me that under some circumstances with some OS's a virus can slip through.