Hi Phil,
Management Reporter with the data mart integration does not require company login as it relies on Windows Authentication for the user. I would suggest upgrading to the data mart option to resolve your password issue.
You are correct in configuring a reporting tree that has company and then department separated out. We do have a suggestion on our Connect site to allow running for reports across all companies. Please vote on this suggestion. You can see the instructions for registering below as well as the suggestion to vote on.
connect.microsoft.com/.../company-as-dimension
Thanks!
Ryan