I was able to do a few things myself. I can use the below bat to sync a directory.
C:\Progra~1\WinSCP\WinSCP /command "option batch on" "option confirm off" "open ftp://user:pass*@server -timeout=180" "synchronize remote D:\Documents /Mine/Documents" "exit"
These will be run manually.
I can do something like this to monitor directories, and the changes are uploaded nearly as the directory changes.
C:\Progra~1\WinSCP\WinSCP /command "option batch on" "option confirm off" "open ftp://user:pass*@server -timeout=180" "keepuptodate D:\School /Mine/School"
I plan on adding the latter script to startup, that way I don't have any question whether or not changes are uploading. And, if I use this vbs script and point to the bat I plan on adding to boot I'll get no annoying prompts or windows.
Set WshShell = CreateObject("WScript.Shell")
WshShell.Run chr(34) & "bat file" & Chr(34), 0
Set WshShell = Nothing
I do have a question though. Is it possible to use the keepuptodate command with multiple corresponding local and remote directories? Is so, how? I'd like to monitor more than one directory, yet only have once instance on WinSCP.com running.