To get the most for your gil, use organic components (their icon looks like a claw or fang) first - until your experience multiplier hits 3.0 (that's as high as it will go). After that, dump mechanic components (their icon is a screw) to the upgraded item.

It's better to use stacks with more components at once, because each component you use also descreases experience multiplier a bit: 30x {organic component} => experience multiplier goes to 3.0 => 40x {mechanic component} (the numbers are made up, I hope you get the point).

Also, keep an eye on the items that are about to hit their experience cap (and become a star-level items), because any experience they get "over" the capacity will be lost in vain.