Not all players use this strategy and with so many bands. This is a strategy intended to be used predominantly in the opening to middlegame. It works best when you have an area with a lot of brown/orange, and have the rest of the puzzle fairly green already. The mojo you get in late game will tend to render this technique less effective. That said it can be effectively used in the endgame at times as well to free up rather substantial amounts of points, but less reliably than early to mid game. Don't be dismayed if it doesn't work right for you, as it seems to, like the rebuild tool, only offer gains occasionally. However this tends to give less random structures than the rebuild tool.
locate an area of the puzzle that has brown, reddish, or orange segments all within the same relative area. They do not need to be contiguous, simply they need to be near each other.
Lock off everything except that area you wish to work on. It works best generally if you press F ( Formally: L key ) to do a global lock, and unlock the segments and sidechains you wish to work on.
After you have isolated the area you wish to work on, it's time to start making rubber bands. Lots of them! Between which points is not that important, in small areas you may wish to link every single unlocked point to every other unlocked point. Don't be shy, 40 or 50 bands is good.
before you move on, save your puzzle! If the rebuild does not go the way you wish, it's much easier to reload this configuration than to do steps 2 and 3 all over again.
Wiggle. For how long depends on your judgment, typically you do not want to let it run long enough to stop changing on it's own. 1 - 8 seconds usually works good, and starting and stopping it again several times in a short time frame give you multiple restore points to undo back to try different configurations.
Once you have a structure you wish to try out, shake first, this is contrary to most other strategies, but seems to work best. Afterwards clear the bands. You may now either wiggle with the rest of the structure locked, or unlock it and wiggle, both seem to work but may yield two slightly different results depending on which you pick.
Once you wiggle it out, if you are worse off than before, you can either try a different configuration if you can undo back to them still, or reload the locked and banded file you saved and try again. Early game it's not uncommon to see 50 - 80 points on a good "manual rebuild" after wiggling it out and tweaking it a bit.