Thank you very much.
oh...boy will this "answer" be a bit of insight on how I do minis...

It depends. Really, on alot. Not the least of which is what I have on my painting table at the time in regards to glue (I hate running to the store for crap like that), and my whim...
For all "clix" figures the base has to go. No doubt. So, I use a new, very sharp Xacto and slice them free at the soles of their feet being very careful
not to to hack off part of the foot (which I too have done a few times). If this happens, I can generally fix it with some creative flocking on the base or something of the sort...

But, to be honest, it has been months since I did that, and it was simply because I was in a rush. I then use GW bases I have added mags to or GaleForce9 mags (my new favorite).
For the Patherfinder and D&D stuff I have been keeping many bases and just gluing mags to the bottom.
Since I mag the bottom of all of my figures, I then generally glue my magnets to the bottom of the figure. Then I will then wash the figures with soapy water (rince very, very well, soap and paint do not mix well). Then I "prime" using a clear, plastic varnish. This allows me to use the paint from the manufacturer as a "rough outline" and they almost always work fine for that (and I am just not that great a painter anyway!)....but I digress you asked about basing.

The glue is the hardest part for these "bendy" plastic bases. But, I have found that my favorite glue on the planet, good, old white "Elmer's Glue" works almost every time. A good heavy coat on the base. Sometimes another light brush over the top if I think it is needed (but to be honest, almost never). Then, they get a varnish coat. I don't flock, etc until after I am done with all painting, so it never has any time to lose *any* flock/sand.
Super glue works even better. The problems with super glue are: Cost, Toxic Odor, difficulty handling as opposed to white clue and the fact super glue will cause a color shift in sand, or flock (to the darker, much darker). All are not show-stoppers, but should be kept in mind. I do like super glue for when I am in a big hurry (of course) and for a base for which I am not entirely trusting my white glue (generally the former, I really do love white glue).
For materials I use whatever cheap flock is at the hobby store when I run out, and a bag of "play sand" from Walmart and a bit of cat litter and plastic plants every now and again. Pour glue on base, then stick it into the baggie of flock/sand/whatever....repeat with 2 or 3 baggies...move to the next one.
Last warning: Seriously, if you try super glue, be careful when you use enough for an entire large monster base or they will find you on the floor under your table some night.

Hope this helps,
Scott