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hi belder,

many thanks for your support and kind words.

1. If my intent is to control BPM, time signature, etc., entirely through Qtractor while running Hydrogen MIDI signals into a track, how should I set the Transport (Master?). Also, transport aside, does it make any material difference if I just set the BPM and time signatures in Qtractor and Hydrogen identically, and avoid the transport business altogether?

I don't if it's still the case but bydrogen jack-transport implementation has been somewhat plagued with issues before, maybe it's better now, i don't know but you can of course try for yourself and enlight me with your findings ;)

let me also tell that jack-transport is not the best there are for heavy beat/loop-based scenarios; meaning that keeping more than one sequencer application in loop-sync is not going to work well all the time for all the cases; it would work best if you stick with one and only sequencer, either qtractor _or_ hydrogen, but not both at the same time, depending on each other, no matter which one you set as master to the timebase (tempo, time-signature aka. BBT info.) it is going to be a rolling open can of worms at best :)

that said, you probably want to have hydrogen as a pure slave/dumb drum-kit sampler instrument--if it accepts MIDI input, which i really don't know--and forget its sequencer capabilities.

2. In terms of overdubbing vs. merging clips. To be clear, if I overdub say, a snare MIDI signal on top of a bass drum track, is that preserved as a separate clip, or does it really just become one clip? The reason I ask is that, is there any advantage in recording and then merging separate clips, other than you can change plugins and such on each separate clip? Incidentally, would it be easier, given my process, to simply create a new track for each drum part and never merge the clips at all?

when recording qtractor creates brand new clips with the recorded material, be that pcm-audio or MIDI, always; thing is, clips may overlap or overlay each other over the timeline; overlapping clips are merged in realtime on playback; you can also merge any two or more clips into a brand new one that replace the original ones (cf. menu [Edit >] Clip > Merge...)

in qtractor, "overdubbing" is actually only supported at the MIDI clip level: see menu [Edit >] Clip > Record, where you may arm and record directly into an existing MIDI clip (you can arm this either from the main timeline view or from the MIDI clip editor (aka. piano-roll view) from menu File > Record.

hth.
cheers

ps. the user manual and howto's are sourced from the qtractor wiki material which is in fact and praise are authored by users just like you.