How do i connect to the ubuntuone couch on the ubuntu server side (the one my local desktopcouch replicates with)
We'll soon be putting together some proper documentation for this. In the meantime, you can use a tool named ubuntuone-couchdb-query to get at your CouchDBs at Ubuntu One. You can download ubuntuone-couchdb-query from http://ubuntuone.com/p/Gyx/.
If you're looking for more technical information (that is, how you'd connect to your in-the-cloud Ubuntu One CouchDBs from your own programs), please clarify your question, and I can explain how ubuntuone-couchdb-query works in more detail.