I tend to do things differently than most it seems (witness some of this topic) so I have 3 stages of AE.
 
Stage 1 - Chests!  I actually start off with 1k cells in ME Chests.  I don't have Iron Chests in my mod list so to get past the double chest stage I have to jump into AE with ME Chests.  As a result I end up with ~4 1k Cells stratified based on my normal chest sorting system.  Raw/Processed mined mats, Tech mats, raw building mats, world/mob drops.
 
Stage 2 - Drives!  Once I get enough Quartz to really start working with AE I'll create a drive and pop those 1K Cells into the drive.  At this point I don't care what goes on which drive.  My only concern is that I have at least one green drive (free types) and all my other drives are orange (full types, free space).  If I run out of types I'll craft another 1K Cell and drop it into the drive.  If I'm running seriously low on space I'll craft a 4K, drop it in, take the red 1K and slap it into an IO Port.  I'll also generally pop the 1K Cell out of its casing so I can use it in a 4K later on, thus saving resources.
 
Stage 3 - Formatting!  Once I get close to running my first quarry I'll set up some preformatted drives for building junk (cobble/dirt/sand/gravel), ores/dusts/ingots.  These will be 4K to start.  Also, this is presuming rev10.n or earlier as in a later revision we're getting formatting based on what is on the drives.  Once we get that I'll actually do a lot more formatting earlier on.