Newbie Question
 

If I book a United flight, but I use partner miles (specifically Turkish), it counts as a United flight right? Like I check in at the United counter and check my bag there and get charged United’s baggage fee, etc?

Correct. (There are lots of airports -- especially in the U.S. -- that are served by UA but not by TK. At those airports, you would have no choice but to check in at the UA counter. It's no different when checking in at an airport served by both UA and TK. If you are flying on a UA-operated flight, you check in at the UA counter.)

You always check in at the airline operating your flight. How/where you bought the ticket and the airline code (on codeshare flights) does not matter.