Hi Kerry,
Yes, this is possible. Each question to your voters is what OpaVote calls a "Contest". Check out our demo election for an example of what this looks like:
https://opavote.com/vote/5654402576678912In the example you gave you would have one election with two contests, one for president with a single winner and one for members-at-large which would have two winners.
I encourage you to run a free test election, simulating the configuration you will want to use for your real election. (Elections are free if you have less than 25 voters and 10 candidates.) A test election will give you a sense for the capabilities of the system, and for the entire lifecycle of an election on OpaVote. You will also be able to make a copy of your test election if you decide to use it as your template for your real election.