I have a small office setup in a remote area with a metered internet connection and am trying to see if Windows Intune will work with WSUS or branchcache or do I have to download all windows updates for each machine through intune itself? 

BranchCache can be used for Intune: http://technet.microsoft.com/en-us/library/jj662699.aspx#BKMK_BranchCache

Using a separate instance of WSUS should be possible, but that then removes update management from Intune defeating part of the purpose fr having it in the first place.