Like Crystal Reports, ActiveReports and other report generators, SSRS has two basic elements behind each report: the SQL query and the report layout. No matter what tool you use for the SQL -- it can be inline SQL in the report or a call to a stored procedure -- it's going to be the same query. Multiple databases are fine as long as you can specify them up front.
You can have parameterized queries, so the user is prompted to input the relevant filters (customer ID, product group, date range, whatever).
Doing the report layout is similar to other tools -- you drag and drop controls like labels onto the report, and set their formatting.
SSRS does provide a lot of options for distributing the report, including email. You can embed the report in an ASP.Net web page, leave it on the report server site for users to browse to, run it in the wee hours of the morning and cache it so every user doesn't have to wait for the lengthy query to run.
It's a great tool. I think it will be worth your effort to experiment with it. I would wait on creating the customized UI until you've exhausted the possibilities inherent in the tool.
Reporting Services contains 2 parts, the SQL instance and the front-end.
If you want to use Reporting Services in SharePoint Integrated mode, you need to create an instance for each farm. However, both SQL instances can be in the same SQL box.
However, the reporting service front-end will need to be part of your SharePoint farm, so this part will need to be separated.
If you're planning to use the old RS webparts (iframe) or access RS webservices through code, you can do anything you want.
Best Answer
It is possible to layer images in SSRS, using the z-index property of images. See http://msdn.microsoft.com/en-us/library/aa275080%28SQL.80%29.aspx