Basically you have 2 choices on how to advance your gear:
1) you can try to get orange gear and improve the mods, either through crafting or by buying mods with commendations, etc.
2) You can stick with normal, non-moddable gear and advance it through crafting, quest drops, commendation purchases, etc.
Both paths should be equally viable, at least in theory, it remains to be seen in if it will in practice. Also, I am not sure if ALL gear slots are moddable - I know you can get moddable weapons, chest pieces and leg pieces, but I haven't seen other equipment slots that are truly moddable (although you can craft exceptional items that take augmentations). The orange armor path lets you find a look you like and stick with it, the other path is going to vary your look as you swap pieces in and out.
In practice so far I have been able to mix both - my sorcerer has a mod-able chest piece, and has been updating that, his light saber and a mod-able weapon I got for my companion buy buying mods with commendations. But I also took synthweaving and have had good luck making a lot of nice blue gear for most of my other slots and for all of Khem Val's equipment, since he basically wears heavy jedi armor.