As I describe it in the manual, the primary use of JaroMail is to keep email local, yes. But as you well mention here there are situations in which it is very handy to have emails stored (or perhaps temporarily moved) on a server.
Jaro Mail so far works also in those situations, substituting the support for OSX-keyring and gnome-keyring with a simple "local keyring" storage using symmetrically encrypted (GPG) entries in an sqlite db. I'm not super-happy about that, but it works for now, it may change in the future.
Anything else is just the same, local or remote. To facilitate moving the stash around I use a Tomb which contains all what's needed - kudos to ZSh for being so lovely and portable, summed up to the small and very common unix programs used, you can imagine I never had a problem moving my setup around on desktops and servers really.
Please also note the difference between the 'peek' and the 'fetch' commands: you don't always need to use the latter, so one can have duplicate setups on servers where only peek is used and nothing is downloaded. Or perhaps one can fetch using the "keep" option as same options as fetchmailrc are supported per-account...