You really do not have much choice in how to meld, for most pieces. The Main Hand Tool, Off Hand Tool, and the Body piece are the three, I think, that you have some leeway on. The rest, you want to max meld as best you can, and that generally means melding specific materia to reach all three stat caps.

For the pieces that do not have attainable caps for all three stats I tend to go CP first, then I'll save the rest of teh room for whatever I happen to need later on. SE has a habit of releasing new recipes with higher stat requirements with some of their patches, and without knowing exactly what the Craft and Control requirements are going to be, I prefer to wait to see them, and to see if I even need to add more to my gear, before filling in those three slots.