Now this is a subject (finally) I know something about; I've got eight of them + plus an old LG12 in bits. On the lower strings (E A D & G) the higher octave string should be the first one you hit on the downstroke. Most nuts will give this away, as they're usually slotted to take the strings, andyway. On slotheads, I start at the nut. The only reason is convenience; the end couple of strings don't get in the way when they're already on. I've had twelve stringers for 40 years, and I still find slots a pain up the arse to restring. Pegs - I also start at the nut end. Same reason; if you start at the other end of the machine head, strings already on get in the way as you work your way back to the nut. From long habit, I tend to take all the old strings off, give the whole box a good clean (Pledge) with a soft cloth, and then replace the strings in pairs starting with bottom E's. If you haven't got a good tuner - leave the old top E's on as a tuning reference until the other sets are in tune. Regarding thumb picking, I can't help much because I'm a flat picker - but I have seen 12 stringers with the E & A higher octave strings removed to help with thumb picking.
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