You’ll need to enumerate the children of the master site and login to each one. You can then use each sites’ ServerId to instantiate a ManagementServer object and access the OutputFolder and other properties for each site.
I made a helper library for myself to wrap the login process, including for multiple sites, as well as generating ConfigApi and ServerCommandService proxies for those few operations not supported in the strong typed objects just yet. Feel free to poke around for inspiration at https://github.com/jhendricks123/CascadiaMipSdkLib/blob/master/CascadiaMipSdkLib/CascadiaMipSdkLib/MilestoneConnection.cs