I usually do them on the morning, before going to work (its a nice way to prepare my mind, by blowing spaceships), then BAM! MaintenanceJust a note that you can now get daily commendations from the top tier space combat dailies as well. Two each for Operation Ascendant Pride and Operation Raging Dawn.
Relics with similar stats (dont even have to be the same stats) will share a small internal cooldown, it will last for the full duration of the relic buff and sometimes a little longer (normally 20-30s), be mindful of that when you use both a defense relic and a shield relic, you wont be able to use both together nor use one right after the other.
If they have the exact same stat, both will go under cooldown together, so dont use 2 defense relics.