The Ultrasound tool is excellent for monitoring your FRS servers, it is however rarely something that we (Microsoft PSS or CTS) use as part of troubleshooting FRS issues that come in.
The reason for that is simple; we usually get involved at the point where a problem already exists and beginning the case by setting up and configuring Ultrasound properly to resolve an existing problem is simply not effective as we have simpler reactive methods of gathering the logs that we need.
I.e. Ultrasound is primarily useful as a proactive monitoring tool and alerting you to when problems arise, it is less useful for telling you why the problem occurred. Our weapon of choice for reactively troubleshooting Sysvol replication problems is usually FRSDiag (or DFSRDiag) as both allow you to gather logs from all your affected servers within a short amount of time.
Documentation for setting up and using Ultrasound for monitoring is sparse but the best resource on setting it up and configuring is probably in the W2k3 Branch Office Guide in Chapter 6, "Using Ultrasound".
If you have MOM available, there's also a special management pack for FRS that builds on the data that Ultrasound gathers.
Windows Server 2003 Active Directory Branch Office Guide (See chapter 6 - Using Ultrasound)
Microsoft Windows File Replication Service 2000/2003 Management Pack for Operations Manager 2007
Ultrasound version 1.0.4080.0 is now available
Monitoring your Branch Office environment
Monitoring Active Directory with MOM
Setting Up Reporting in the Windows File Replication Service Management Pack
File Replication Service (FRS) troubleshooting tools
FRS Tools and settings
Microsoft Windows DFS Replication Service Management Pack for Microsoft Operations Manager 2005