I suggest when doing this achievement you start with the first 3 sectors to get it out of the way. All you have to do is for each sector is finish a couple side missions and then do the regular missions. For each mission you will get a certain amount of morale. If you press back to find the mission you can highlight it and it will tell you how much morale you will receive for completing the mission.
Remember that you only have to raise the morale to 100% once for each of the sectors, it doesn't matter if they drop in percentage as it still counts.