Honestly as regards your first point it doesn’t require that at all. DEVONthink 3 can be overhauled and totally reconstructed quite easily. I have done it a few times. I really suggest that one gets stuck in. I am also going to recommend MacSparky’s field guide. I am a long time user of DEVONthink 3 but I found, as I always do with David, that there was stuff I didn’t know. Also it is laid out in a very clear way. I use the Field Guide as a reference already, rather than a step by step introduction which I don’t really need. It is 49$ well spent even for a long time user.
Really though, believe me, you don’t need to fix a workflow at the start. The opposite in fact I would say. DEVONthink 3 will help you if you work with it.