Yes -- opam and dune are complimentary. I normally use dune (formerly known as "jbuilder") as the build system within my packages, which I then publish and install via opam. Dune does the fast incremental builds, while opam deals with version constraint solving, downloading and general package metadata.

There are some interesting experiments combining the two more closely -- take a look at "duniverse" https://github.com/avsm/duniverse which is a prototype system which would use opam to solve package version constraints and download the sources, allowing dune to build everything at once. The nice thing about this is that you could patch one of your dependencies and then dune will be able to perform an incremental build, as if all the code was in one big project. I'm personally hoping this will help speed up Mirage development as it can be time-consuming to propose a change to an interface and then find all the places that need changing (a cost of having lots of small repos versus a big monorepo)