How do I seal between the soffit and frieze board?
In this case, a caulk that matches the dark frieze board will probably be least conspicuous. You should be able to find a silicone or urethane that's very dark but not black. It might be called "dark walnut", or maybe "charcoal gray". 

I'd avoid latex caulks as they don't bond particularly well and they shrink substantially. 

If the cavity is deeper than 3/8" or so, pre-fill with foam rope caulk to act as a backer.