The IM/Online thing is for when you get into combat only.
Basically, the plan is to send a map screenshot and then exchange orders and results in realtime until the tactical combat is over.
As of yet, it has not been used. The one military incident so far involved a ship with an NPC captain.
Basically, as a military officer, you get full control over the ship you are on. The Minister of Defense may promote you to a fleet commander or admiral or whatever, which would give you direct control over additional ships.
You only get to use Tactical combat if you are personally in the sector.
As a military officer, there is also an experience system, so as you explore new systems, train at planetary facilities, and perform heroic acts, you'll be given the opportunity to purchase upgrades to your avatar. Hitpoints/Shields, Damage amount, ECM / CS.
These only have direct effects on the game during ground combat, but they're nice to have.
The ECM and CS bonuses can have a particularily large effect, since it will be applied to all thr troops on the planet with you.
You could forseeably make a career just on ground combat alone, though you'd probably be given command of the troop ship on the way over