As it currently stands this is not possible, all the custom taxonomies are displayed from a loop so inserting it in between two specific fields is a bit difficult at the moment, this is something I need to include in a future version.
To put the search field after all the taxonomies (not sure if this really helps at all) I would open search-filter.php and move the if block that start if($search==1) around line 667 after the foreach loop immediately following that. This would at best move the search field to the bottom of the list.
I’ll look to including this functionality in the next release – shouldn’t be too hard to integrate, thanks for the feedback 🙂
