Using all 64k disks is a huge waste of resources if you're storing items that you don't have many of, or don't stack. Big disks can still only store 63 different item types. Sure, in the late game, resources aren't an issue, but I'd never start out with only 64k disks.
What I tend to do is make a few 1k disks, and import those items that I don't have many of first. Since I'm fairly organised about chests before I have AE, that's generally pretty easy. Then I add a few 4k disks, and some formatted 16k disks for bulk storage where I'm not using barrels or storage drawers, moving to 64k disks later on.
Another useful tip if you have ExUtils is to add an advanced filing cabinet via a storage bus (raise the priority), and get all your non-stacking items into that, with an IO port if necessary. Saves a lot of item slots.
As for when I start on AE, usually shortly after I have a stable power supply of a few hundred RF/t and a few stacks of certus/nether quartz. If I'm still in a temporary base, the system is likely to be very rough & ready (drive plus crafting terminal and not much else)...
