When you upload your PowerPivot for Excel workbook to your PowerPivot enabled SharePoint site, you typically will deal with much larger files than your other SharePoint sites. This is the reason why we suggest that you increase the Excel Services and SharePoint to the max file sizes allowed (to do this, follow Step 18 at http://powerpivotgeek.com/server-installation/existing-farm-install/).
Saying this, there are some other quick tips as well:
The SharePoint Server local cache is the c:\windows\temp\WebTempDir. This folder can fill up real fast so you may want to clear out this folder every so often and/or aim the local cache to another folder altogether
By default, SharePoint keeps all documents even after they are deleted within the SharePoint content database for up to 30 days. This means your content database may significantly increase in size if you upload alot of large PowerPivot for SharePoint files. Therefore, to fully delete SharePoint documents and free up space, you need to delete them from three places:
1. Delete from the document library.
2. Delete from the recycle bin of the site.
3. Delete from Site Settings -> Site Collection Administration -> Recycle Bin (note that you need to be a Site Collection Admin in order to do this).
4. Also delete the files within the Deleted from end user Recycle Bin. This area allows you to restore and are automatically deleted in 30 days. But if you need the space now, then you should delete this as well.
In a future blog posting, I will also talk about the issues concerning SharePoint file uploading and potential optimizations for upload.