Make sure you have back ups of everything before you start. That is what experience taught me. I think it is good practice to back up before any large scale changes on Macs anyway? The reason in this case is that one can make some bad user error things at first and it is possible to scramble your files in various ways, I always got them back but once I did use, for speed, a backup: I made some silly ‘smart rules’ for example that executed literally once. I forget the details.
Then drag and drop wholesale. It is a long time since I did it, I put everything in DEVONthink 3 straight away, even screenshots go into the Inbox and get moved by a smart rule from there into another database. I don’t index much and haven’t found a lot of use for it myself and I only recently made some tags. I think it can get confusing and it is best to add things, even at that grain, as you proceed, even afer months or in my case years.
BlueFrog already said everything anyway. As for number of databases, from reading here there seems a lot of variation, depending on what you use it for. I keep it to about 8 I think, I avoid making them too big as Bluefrog says.