Hook the VPC up like normal, then put the e-Manage in between the VPC and the ECU. You want to do it this way so the e-Manage can clean up the "dirty" VPC frequency output. Also use the e-Manage for all of your tuning as it is much more flexible, you simply need the VPC to remove the AFM.
No, you want to put the e-Manage on the line that the VPC sends to the ECU. In other words, you want the e-Manage on your KV freq stream, not the MAP stream. The VPC should have 2 AFM related wires, one that runs from HKS's pressure sensor and the other that runs to the ECU which tricks the ECU into thinking the KV AFM is still there. Unfortunately the signal the VPC sends out is a little choppy and distorted sometimes, but the e-Manage will automatically clean it up a little for you.
Profec e-01 is definitely the way to go in combination with the e-Manage.
I changed mine around the other day going from psi sensor to afc to vpc to ecu to running psi sensor to vpc to afc to ecu and the difference was amazing, especially at idle. The car runs better now with 680 injectors and this set up then it did with the Lex/550 and the tuning screw. From what I understand the e-manage does an even better job than the afc.