It depends on the particular flake. For what I'd call "well-behaved" flakes (not super dense or moist) like OGS, any Solani, Capstan, Stokkebye LNF, etc. I dry the flakes whole just slightly. Then I fill the pipe with a combination of mush/fold-and-stuff at the bottom and more rubbed out tobacco on top. But for denser, moister flakes (Sam Gawith, G&H, some McClellands), I find that whole flakes don't dry evenly and take forever to boot. However, I also find they don't always rub out evenly straight out of the tin either. So I might dry them briefly (~20 minutes), then rub them out, then let the rubbed-out tobacco dry as long as necessary.