I use FreeAgent for my Zweigniederlassung. I export my bank transactions from Volksbank's web interface, convert the file with a script I wrote (https://github.com/airblade/volksbanker) and upload into FreeAgent.

FreeAgent doesn't integrate with Datev or anything like that. However my Steuerberater can log into my FreeAgent account and get all the book-keeping information he needs.

Http://debitoor.com