There are two ways to get energy, burn fuel, or collect by energy collector.
If you look top right, you see the static fuel cost. This is fuel that is always spent. In addition you can poke around seeing the fuel used by the engines, hyper drive, and all weapons firing.
In general, you want enough reactor output to do all things at once, except the hyper drive. Cover static cost, sprint at full speeds, add a little bit for shield recharge, and fire all weapons at full.
Where does energy collectors come in for a ship? In not spending fuel while sitting idle. So on a military ship (or civilian) it is a good idea to have enough energy collector to cover the static cost. This means that the fleet you parked in your home system with full fuel tanks will still have full fuel tanks when you need them.
Bases are a bit different, you typically want to cover the daily life and then some with energy collectors.
But Nedrear: Are you sure there is no energy to collect in gas clouds? I am pretty sure I don't run fuel transports to keep bases in those alive, or that military ships parked in a gas cloud uses fuel (with energy collectors).