- Starting out, don't worry about any mothership modules apart from crystal and metal gathering. Build the others to collect the training rewards, but focus on these two. (I'll post a queuing guide next)
- Do the first adventure - that will give you a new commander. The next commander is a ways in. Best to hit those with better tech.
- Find a governor and a main fighter.
You want a governor with metal or crystal skill (ideally both, but that rarely happens). Fuel is useless. Crystal is needed for research, while metal is needed for advanced flagships.
Your main fighter will have tempest skill (and ideally vulcan or destroyer). This is because the computer guys love fighters and are optimized for killing cruisers and battleships (and fighters are too flimsy for big fights).
You will get fifteen commanders over time, and have upwards of six planets (each needs a governor). You will want a battleship commander, and Longbow commanders are good for killing enemy player's flagships.
Use your experience potions on your governor (your fighter will get plenty of xp from fighting). Don't worry too much about rank at first. You can rank up your governor with medals a couple times to get him more points for politics skill and his resource specialization.