I have a working setup as you describe, with a 2-way
diseqc switch.
The switch goes after the motor, and before the LNBFs, since you want to be able to move the dish regardless of which LNBF is selected by the switch. The input of the switch is connected to the LNB side of the motor, and the numbered outputs of the switch each go to an LNBF. I put my universal (linear) LNBF on switch port 1, and the circular on port 2. I attached the switch to the feed arm of the dish, with short jumper cables from the outputs to each LNBF. Works just fine.
In my receiver, a Fortec Lifetime Ultra, for each satellite, diseqc is enabled with either code #1 or #2 as appropriate (linear or circular). There's also a motor position offset to deal with too, but hopefully you've already worked that out. I made a multi-LNBF bracket with a dollar or two in parts from the hardware store.