I would go on about organizing my empire's military as such:
I would begin with a colony. Undeployed (as in still on the colony) troops on that planet would be a part of a planetary army reserve/national guard/paramilitary unit with policing powers (limited or total, your choice). Undeployed fighters on that planet would be a part of a planetary air reserve/air national guard serving its home planet. Undeployed Sats, mines, and drones would be maintained by an invisible planetary armory or a network of them, controlled by a Imperial logistical command of some sort, with the emperor having the ultimate say in their deployment. Weapon platforms would be the responsibility of a planetary air defense command (NORAD on a global scale), which in turn would be a part in a huge network of planetary defense commands in your empire.
Moving on to the planet's orbit, satellites and mines deployed in orbit would be under the command of the planeatary NORAD I just mentioned above. Some satellites such as recon satellites would be under the control of the Imperial Starfleet, or perhaps under the control of an Intelligence service, should there be one. Military Bases in orbit would
not be under the planet's jurisdiction, and would be handled by the Imperial starfleet, which are commanded by a base commander, or a base command AI unit.
Space yard bases and/or repair bases could be controlled by private companies. Any troops that have been loaded onto a transport is now considered active, and is now under the direct control of the Imperial Army (which is under your direction). Fighters loaded onto Carriers are also now under the control of the Imperial Starfleet. Mines, Sats, and drones loaded onto their respective carriers are also under the control of the starfleet, or that logistical command once more, awaiting to be delivered and deployed. Deployed drones would be controled by the Starfleet.
Moving onto outer space, Bread and butter warships and fleets of them would be under the control of the Starfleet/admiralty/navy. Population and Troop transports would be under the jurisdiction of the Imperial Merchant Marine. Ships with boarding parties would be under Starfleet control, but specifically under the control of a Starfleet Marine Service. Carriers would also be under the control of the starfleet. Specialty ships, such as Space Yard Ships, repair ships, medical ships, minesweepers, mine and sat layers, drone launchers, supply tankers, and such, would be under the control of the starfleet or special branches made for controling such ships. Mines and sats deployed over empty/enemy planets and/or warp points would be under the control of the starfleet.
Which all comes under the emperor's jurisdiction.
I hope my little post here answered some of your questions.