For starters, these engines don't like aftermarket thermostats. Some people have reported success with them, most people have problems.. You should have used a the motorcraft thermostat thats specced for these trucks.

For the radiator hose question, yes thats normal. The hot water goes into the top of the radiator, and cold water comes out the bottom. The radiators on these trucks work really well. Also, since your thermostat isn't working right, its not dumping as much hot into the radiator.

I believe there is a ball in the thermostat neck that works as a checkvalve, and that will bleed the system for you. But I haven't had one apart so I can't tell you specifics, do a search or wait for other replies.