Longpoll is currently not implemented in the bfgminer getwork proxy, so that will result in low efficiency / lots of stales. Using slush's proxy, cubes do appear as separate workers to the pool when running a single instance of slush's proxy, however, I can't recommend that either. While playing around with slush's proxy and the stratum-mining pool software, I discovered that if you have multiple cubes connected to one instance of slush's proxy, then the proxy will get the share difficulties confused and only submit shares that meet the highest difficulty requirements of all workers.
I'm interested in this - how did you determine this and how much of an effect do you see? I use slush's proxy except for p2pool sites. I currently run one proxy that serves two Blades and another proxy that serves 5 Cubes. I do notice that my Cubes run faster on slush's proxy than on bfgminer - fewer stales, but still not as high an efficiency number as my Blades.
The pool server software shows each accepted share and that share's difficulty. When I had two cubes going through a single instance of slush's proxy, the pool server software adjusted the share difficulty to each cube, and somehow it managed to assign a difficulty of 10 (ten) to cube 1, and a difficulty of 100 (hundred) to cube 2. I noticed in the pool software terminal that cube 1 was only submitting shares of difficulty 100 or higher even though the pool share difficulty was 10 for that cube. Using two separate proxies fixed this.
Here's the faulty setup:
[cube 1 and cube 2] --> [slush's proxy] --> [pool server]
Here's a setup that works:
[cube 1] --> [instance 1 of slush's proxy] --> [pool server]
[cube 2] --> [instance 2 of slush's proxy] --> [pool server]
etc..
I don't have enough stats to say how much effect this really has... With two workers that have the same hashrate you would think that the pool server would give out shares of the same difficulty to each, but that is definitely not the case with slush's pool or the stratum-mining pool software I've been playing with. More info on the pool server software:
https://bitcointalksearch.org/topic/avalon-users-bitcoind-and-slushsgeneralfaults-mining-pool-setup-162788