I've got the ES stage 1 and 2 kit.
Yes, run the wastegate off of the upper intercooler pipe. Kevin explained that this location would reduce boost creap.
I'm running the dual valve set-up as well with the wastegate leading to the upper intercooler pipe, the HKS connected to the brake booster, and the stock BPV and boost gauge connected to the intake manifold vacuum source.
DSM - the HKS is more than capable, but running the dual valve set-up with the ES system will eliminate the stalling problem and the compressor surge.
If you choose to install the MBC, then you would place that in the line that leads from the intercooler pipe to the wastegate.
I have never installed this on my car because I am more than happy with its performance even thought my car only boosts 5PSI stock.
Hope that helps.
Mark