That is pretty much how it'll work depending on your reader program. If it supports pointing at a directory, then yes, that'll work fine. Or you can just use LegerCalibre to view the library on all the Android devices and when you tell it to open a book, it'll open in the program set for the file type.
So, for my eDGe, I sync using Dropbox on my PC and DropSync on my eDGe, then I just fire up LegerCalibre and use it to browse my library. When I find a book I want, I just open it and, depending on the format, it'll open in say PerfectViewer (for comics) or the eDGe Library app for ePub, or Adobe Reader for PDFs.
I haven't tested out Moon Readers Dropbox support yet. I've been happy with this setup, so haven't felt the need. Oh, ES File Explorer (comes in the ROM on the eDGes) supports Dropbox directly, as well as a buncha other online storage systems with the latest versions.