Hello,
First of all: this plugin rocks! Take a look Woontrendz.nl which works with this powerful configuration:
1. WP Engine hosting
2. MaxCDN content delivery network
3. Autoptimize combine/minify
Page load time: 511 ms (Tested from Amsterdam, The Netherlands)
Second: I also have a suggestion for improvement of the AUTOPTIMIZE plugin.
As far as I know there's no option for Javascript files to be both combined/minified in the header and footer of the website. If you want to keep the header scripts in the header and the footer scripts in the footer, it's not possible.
The only solution the plugin offers is to place the minified file in the head or the footer.
Why not create an option that allows one to create 2 minified JS files. One for the header scripts, placed in the header, and one for the footer, placed in the footer.
Cheers!