I would be interested in knowing this as well.
Unless you deleted the uploads folder, I think you can leave them be.
What I did was move them to wp-content/blogs.dir/1/files/YYYY etc (blog 1 being my main blog) and then tossed this in my .htaccess:
# Moved Images
RewriteRule ^wp-content/uploads/(.*)$ http://domain.com/wp-content/blogs.dir/1/files/$1 [L,R=301]
Alternately you could search/replace on your database, but I’m lazy.
You will also need to tell Blog #1 that it now stores it’s files in blogs.dir/1/files/, there are a couple places to manage that, so look through the http://domain.com/wp-admin/ms-sites.php?action=editblog&id=1 (where again, 1 is the blog number) interface.
Oddly enough, the files have all been imported, (these are images from another blog that I did a WP export on, then imported the exported file into my 3.0 multisite blog), so they’re in blogs.dir/{id} already – except on the “main” blog of the site, (id 1), since I upgraded from WP standalone, not WPMU. Its files are in wp-content/uploads I tried moving its files to blogs.dir/1 but it seems to have a database setting somewhere that tells WP that the files are in wp-content/uploads, so that didn’t work too well.
I added this to my .htaccess:
RewriteCond %{HTTP_HOST} !johnbeales\.com [NC]
RewriteRule ^wp-content/uploads/(.+) wp-includes/ms-files.php?file=$1 [L]
johnbeales.com is the site with ID 1, so it gets its files from wp-content/uploads, but everything else goes to blogs.dir. So far it’s working, if a bit hackish.
I also found that since I had been using a custom thumbnail size that when the images were imported they were not imported at the correct size, so in addition to my path issues I had bad filenames. The Regenrate Thumbnails plugin solved this for me.
I’d still like to not have to be hacking around in my .htaccess, but at least it works now.
Alternately, you could manually create the 1 folder, move the files, and make the changes. I just wrote a blog post about this, after thinking about your problem: http://code.ipstenu.org/moving-your-images-for-multisite/
