Once the shoots get long enough to twisty-tie, you can start. For an LST, I'd recommend training the side branches, and cull (remove) most the branches that are coming from the center of the plant, and/or those that are aimed twords the center of the plant. (depending on how many shoots you want to keep for the LST) They'll just get in the way later, or can develop into mainstem(s), making it more difficult to keep an even canopy.
Yes, it's true that the tallest branch (closest to the light?) get's all the glory. Something to do with the formation and use of certain auxins (hormones) in the plant, but I have no clear understanding of how the plant knows which branch to choose as the mainstem replacement(s). Possibly it's from quantity of light recieved and length and health of the stem, or perhaps it's the stored nutrients in the leaves...but I'm guessing here.
Trimming the roots after harvest is easier than the following process, but here's what I've done to successfully correct this situation...
Firstly, do you have a 15 gallon pot in case the roots go crazy?
If not, in emergencies I'll lift out the semi-dry rootball, (wet rootballs fall apart) add an inch or two (see below for how much) of fresh soil to the bottom of the pot, replace the rootball, add whatever soil I can get between the pot and the rootball, and water it all in. Gives a small percentage of extra space, but is a band-aid and not something you'll want to do every grow. But if you're careful it works better than dealing with rootbound issues for the second half of flowering, and might just give 'em a comfortable flowering cycle.
However much space you have between top of rootball, and the edge of the pot before doing all of this, is a good way gauge the ammount of soil you can add. Make sure to leave an inch or so for future waterings.
Did I explain that ok?