I use my fretting pinky quite extensively... especially for long stretches and sometimes for slides down towards the bridge. There's an 'ideal' finger configuration for each tab - most song books and teachers would tell you which finger is the most economical to use from which postion.
I must admit, the pinky is quite weak in comparison to the rest of your fingers, but if you force yourself to use it, it'll be up and running in a few weeks / months without a problem!
I presume you mean putting your thumb over the top of the fretboard to hit the E string? imho, wrong! Never done that... v bad habit to get into if you ask me

But then again... I'm no teacher...