We are working on slots and cutouts for PCB123 v5.
The best way to include the notches in the corners of you board is to make them part of your board outline. If they are part of your outline they are not counted as cutouts unless they require routing with a < .062" router. If you have a large hole (< .25") you can include the appropriately sized hole as part of your drill file. If you can't include the information on your drill file you can add it to the board outline layer or on a separate fabrication layer.
It really depends on the software you plan to use. If you are using PCB123 you can include the information on the mechanical layer. Remember that you can't order slots and cutouts through PCB123 yet so make sure you go to PCBexpress/Quickturn
to place your order and use PCBexpress for <= 4 slot and cutouts or Full Feature for > 4.
Eagle: Include notches as part of the board outline. Overlapping drill holes are fine for slots and you can place cutouts on the dimension layer.
Allegro: No native file support at this time, but you can generate your own gerbers.
Altium: We have native file support up to version 10.
Please contact [url=http://www.sunstone.com/pcb-solutions/p ... ols/pcb123