Always focus on upgrading projects.
If there are no upgrade projects or it is already running then focus on the other projects. It is only logical to focus on the one that is closer to completion.
If none of them are closer to completion then just put them wherever you want.
Of course, keep an eye on the starbase message of the day. If there is anything I need to tell you about the starbase, it will be there.
I always put my fleet marks toward station upgrades first, then main projects, requisition projects, and special projects last. That way I am focused on moving the fleet forward.
I try to do the same with duty officers, except that if I have a choice between putting a specific officer in a specific slot, like Sensors Officer, or a general slot like Military, I fill up the specific slots first. That way whoever comes behind me will have a wider choice of available officers to fill the vacant slots.
I've also tried to watch what DOFF missions I accept. Any that require officers that show up as requirements on the Starbase I limit to DOFFs who are already bound. That way, I keep as many as possible available to contribute to the Starbase projects. Unfortunately, before the Starbase started building, I (like many of us, I suspect) converted almost all of my common DOFFs into uncommon DOFFs, most of which aren't used on the Starbase very much. Now I only convert if we really need a particular DOFF, such as uncommon Diplomats.