Well we need an example of what you are using.
with ATX, you will have back panel IO and also a 20pin connector.
With BTX (The like 1 board that uses it so far) just has a 24Pin connector and the Processor is in the lower right hand side of the board.
With AT you have a dual inline 8 prong IIRC plug. like this: ---- ---- Also will have a weird back panel IO.
-Kevin