One of the reasons it's not a good idea to bring any other "modes" into Link and Amp is that for the Eywa award, "Extend Time" on the mode takes precedence over "Add-a-ball" for the MB. Nothing sucks more than you hit Eywa to resurrect your mb, and it awards "Extend Time" on Bomber Battle or Seeds instead. Also note that in tourney mode, the first Eywa award during Link mb is not add-a-ball, however, it is the first award during Amp mb. So the ultimate sequence to get to the double-double Link is to start Link. collect Eywa as soon as possible so you can hopefully reload it for the Link add-a-ball. Drop the visor for Amp, and prime it. If you make it through to the double-double, then great, otherwise, you can then stack Amp in to keep Link going with a new ball saver. And you know the next Eywa award will be an add-a-ball, too. By then, you should be very close to the Super on Link and getting to the Link double-double is "The Thing", so it's absolutely good value to extend that mb, if necessary with Amp.You can only get one double-double during an entire Link - it's victory laps from then on, but a double-double Amp super is nothing to sneeze at either, and you can do those over and over in the same mb.
If you just want to play for fun and get to Final Battle, everything is trivial to light except for the Navi light, so concentrate on finishing your Navi characters and getting Navi MB lit and then qualify the other shots. Once you're ready to go, play Navi MB last (that way, if you drain before it starts, you can reload everything else again relatively easily). Don't double drain out of Navi MB at the end (lol) and then play the Final Battle "skillful drain"-fest... And remember that it's not just about completing "levels" in Final Battle, it's about finishing the switch hits, and then super skillfully draining the remaining balls out the outlanes for the Unobtanium awards before starting the next level...
As always, ymmv.