Ok I found the answer somewhere in this forum. I wanted to change my upload directory wich was pointing in the middle of my collection.
I use the following sturcture MAIN/GENRE/ARTIST/ALBUM(S)/TRACK(S). 69 Genres, +4000 artists, + 17.000 albums, + 220.000 tracks. The Incoming folder was placed as a "main/incoming" folder, it always worked but after upgrading to 4.8 The Incoming folder was placed inside the first genre (main/genre1/incoming). To manually override these settings you have to find the "more.js".
subsonic\jetty\3434\webapp\WEB-INF\jsp\more.jsp Open the more jsp in your editor and find the part (in my case rule 140)
<td><fmt:message key="more.upload.target"/></td>
<td><input type="text" id="dir" name="dir"
readonly ="true" size="37" value="
${model.uploadDirectory}"/></td>
replace ${model.uploadDirectory} with the folder within your main music folder f.e. I:\ALL MUSIC\Incoming
<td><fmt:message key="more.upload.target"/></td>
<td><input type="text" id="dir" name="dir"
readonly ="true" size="37" value="
I:\ALL MUSIC\Incoming"/></td>
Add the Incoming folder by setting it as a media folder (settings -> media folder new folder Incoming = I:\ALL MUSIC\Incoming)
Hope this will work for you, it worked for me