Assuming your switches are stacked, you should be able to bond the interfaces on the Linux side and configure etherchannels at the switch side. This will provide you a single, loadbalanced and resilient link incorporating the two interfaces.
If what you are after is having two separate links and your question is about trunking multiple VLANs over those links (as you would with a XEN host) then all your config will be in /etc/network/interfaces, configuring subinterfaces for every VLAN required.
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