is there anyway to check your winnings from showdown/non showdown pots by position/hand?

Not yet on a single graph, no, but you could use the Filters button to filter to the hands/positions you want.
If you expand the graph (or any report) using the little 4-arrow icon to the right of the report it will stay open as a snapshot which won't update so you can then change filters and compare the next graph.

Is anyone else somewhat underwhelmed by the graphing abilities of PT3? I could easily be missing something, but it seems like the only options I've got are the three graphing choices...the only one I like is the showdown + nonshowdown + overall graphs.

can you give me a se by set guide of what i need to press to do this. i havent really got my head around the filters part.

Graphing functionality is still somewhat limited, yes - graphing options will be added and it will eventually be fully configurable like the other reports.

Click the Filters button, and on the first page (General tab) in the bottom left, you will see a 'Position' section where you can set the criteria you want to use.
e.g. if you only want to see hands when you were on the button, you would set it to Postition Off the Button 'Exactly' 0.
0 is the button, 1 is the cutoff, and so on; the BB is always 8 and SB always 9, regardless of table size.

To select only hands where you had certain hole cards, use the 'Hole Cards' tab.