In the MarketPress documentation is states that

In the Paymenttab select your payment gateways and configure each payment option you've chosen.
The Payment gateways displayed vary depending whether MarketPress is installed on Multisite or not.
When in Multisite the gateways allowed are controlled in Settings > MarketPress in the network admin dashboard.

I can't seem to find it in wp 3.3.1 - is there a secret?