You need the -gp option on the stratum proxy, so each one is listening on a different pool.

mining_proxy.exe -o pool1 -p port1 -gp 8332
mining_proxy.exe -o pool2 -p port2 -gp 8333

Configure your pool1 blades to Ports 8332,8332 and the pool2 blades to Ports 8333,8333

I had a setup exactly like that running for a day earlier this week, mining for a friend; two stratum proxies on the same machine pointed to different pools.