I've travelled with friends before (BF and I don't really keep track of who pays, we're pretty good about taking turns), and it may be a little tedious, but when the bill comes, we just separate everything out right there -- I'm also like the group "accountant" so I usually figure it out for everyone. So I'll add up whatever food and drink I ordered, plus my share of any appetizer(s) we may have ordered, and multiply by, as an example, 1.23 percent. The 1.23 comes from at least a 15 percent tip, plus in this example, 8 percent tax. It sounds complicated, but if there's just two of you, it should only take a couple minutes.
The other idea is for the two of you to work out a food budget now. For example, let's say for the whole trip the two of you will spend up to $500, so if you split that in half, each of you is responsible for $250. You can just keep a small piece of paper with $250 on the left for you, and $250 on the right for him, and whatever meals you pay for, deduct it from your $250, etc.