I am looking to rewrite urls with multiple substrings. One substring is being requested as a subdirectory, while any others are requested as normal query string parameters.
The query is not part of the URL path and thus cannot be processed with the RewriteRule directive. This can only be done with the RewriteCond directive (see %{QUERY_STRING}).
But as Chad Birch already said it suffices th set the QSA flag to automatically get the original requested query appended to the new URL.