What monitors are you planning to run and what inputs do they have?
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You can do this. I connect a Dell U2412m to my thunderbolt port on my MBA and Mini (using a miniDP to DVI adaptor ) or to the HDMI out on my mini. I can also connect a Dell to the HDMI port and an ACD to the thunderbolt port at the same time.
On the rMBP you have three outputs (2x TB and 1 x HDMI) and you can connect any modern monitor to a thunderbolt port
That means you can connect any two displays via the TB ports (using miniDP to DP or miniDP to DVI or miniDP to HDMI connectors) and then another display using the HDMI port.