I have an amplifier for my antenna with two outputs. If I don't have anything plugged into the second port, am I causing any problems with feedback or other voodoo RF things?

What make model amp?
If you have/see problems, you can use one of these:
http://www.techtoolsupply.com/index.asp?PageAction=VIEWPROD&ProdID=511

I have an amplifier for my antenna with two outputs. If I don't have anything plugged into the second port, am I causing any problems with feedback or other voodoo RF things?

not really....but its a good question....an open port will increase the SWR (standing wave ratio) of the system....high swr is bad...low swr is good....however, swr is usually only critical in a transmit circuit and not in an antenna receive circuit like u have....

the link Ratman gave shows a terminator....its just a 75 ohm resistor which will 'terminate' an open port, which helps keeps the system swr desirably low....so ideally u would attach a terminator to the open port...if u can find some terminators always use them anywhere u have unused/open ports....