For maximum efficiency progression: Do the 1k XP Projects, other usefull projects (in early stages) are Ship Requisition I (after you have shipyard I) and Requisition personal science and engineering II (fabricator and sensor array II), these give you the most for your money(dilithium).
IGNORE the Buff and Operational assets projects, IMHO these are not worth the invested money (and drain your fleetmarks, and most important medical(!!!) and operations personal, from the more important 1k projects).
For DOFFs:buy them for fleetcredits, when buying sciens department DOFFs, save the science ones for the starbase/science upgrades, execute the remaining Sci DOFFs.
Fleetmarks: Do nukara as long as it still provide fleetmarks.
Provisions: Check STOWiki for cheapest sellers, it will save you a LOT of Credits.
And finally (well, as a personal opinion) ... DON'T give Administration rights to subordinates, because too many cooks spoil the broth.