There's probably a better way but I would do the following...
Make a "blank" vbulletin page (there are articles on how to do this) call it something like upload.php...
In the UPLOAD template you make as part of step 1 make an iframe that points to the phUploader page you already installed.
This way people using phUpload will look like it's all being done within your forum- it will have the common header, footer, etc..
Finally make a custom BB Code that auto fills in the URL to wherever the files are uploaded, if they are images something like:
Code:
<img src="http://www.yourdomain.com/phUploader/files/{param}" />
You can give it an icon so users can simply click on it in the editor to insert a file...
It's not super-integrated but it would work.