Working on 1.9.0 and the default setting will be to put optimized CSS before the opening and optimized JS-forced-in-head after the closing title-tag.
The API will allow to change that behavior, allowing you to specify a tag and whether to put the optimized CSS/JS before or after that tag or to simply replace it (allowing you to put e.g. <injectjs> in your theme, which would then be replace by the optimized script-tag).
I'll ping you here as soon as a "beta"-version of 1.9.0 is available, would be nice if you could test.