The standard layer never bothered me (other than Fn location), but the function layer is all kinds of messy IMO.
I'd change Control to Function, then map Fn+C, Fn+X, Fn+Z etc, to Ctrl+C and so forth, then setup Fn +IJKL to arrows, Fn+U to pageup, Fn+O to page down. Basically mimic the Pok3r movement function layer, as I find it the easiest to use. Then I'd map the following keys like this:
Command keys -> Alt
Left Alt -> Ctrl (for any Ctrl+ commands not in the function layer)
Right Alt -> Windows (For Windows+L, as that's pretty much the only Windows key shortcut I use).