The SVN Repository Details "Folder" seems to have to be a actual repo; you can't shorten it to leave out the repo name. Does this mean I can't use Agent SVN to work with two projects that are in different repos (even though they are on the same svn server)?
It seems like the config should be allowed to just put the svn server root in there, and not have to specify a single specific repo. Or maybe just allow full paths to repos in the per-project Scc_ProjName property (to override whatever is configured globally)... detecting a protocol on the start of the Scc_ProjName should be easy enough, right?
How to use multiple repositories?
Does this mean I can't use Agent SVN to work with two projects that are in different repos (even though they are on the same svn server)?
No, but first let me explain some details.
Agent SVN implements the MS-SCCI inteface.
The MS-SCCI links a project to source control through a process called binding and you only have to bind a project once.
In MS-SCCI the binding defines the location of the project and is made up these two parts:
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Project Binding = Aux Path + Project Name
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Aux Path = Subversion repository root location
Subversion URL = Aux Path + Project Name
Now when you bind the project for the first time the project name is obvious.
But what about the Aux Path?
What Agent SVN does is define a default Aux Path in the configuration utility.
So when you bind a project Agent SVN use the project name and the default Aux Path to create the binding.
So back to the question of how to have multiple projects in multiple repositories

What you need to do is this:
1) Start the Agent SVN configuration utility
2) Point the AUX Path to the first repository
3) Open the first project
4) Bind that project to the repository making sure this rule is correct:
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AUX Path + Project name = full URL of subversion project
Because the binding only have to be done once, those details will stick, no matter what other Agent SVN configuration changes are made.
Cheers Jussi