If you can log in using WinSCP you definitely should be able to also use PuTTY as they both use the same protocols and ports, one just handles files while the other commandline. But, you should also be able to physically login to the system locally on the system itself. If you used the official MineOS Turnkey distro the way you do so is with [ALT]+[F1] keys pushed at the same time (…well actually this also applies to other distros such as Ubuntu, Debian, and quite possibly every other distro…), and you should get a login prompt. If not, hit enter and one should appear. Login using the same credentials you would when using WinSCP and from there you’ll be able to follow @iMelsom’s steps.
One thing I would advise however is to temporarily stop the web ui from running or to temporarily disable it from starting up with the OS (or both) for the time being, if the system is feeling a bit sluggish. Doing so will allow you to have nothing running other than OS essentials and should feel a lot snappier if your current configuration eats up all your system’s resources (or a majority of it with not really much for the core system itself to run with).
Another thing, this is kind of a known problem when using Dynmap, and you may want to see this which may be of assistance with dealing with/solving it: Potential MineOS Web UI Lag Fix for Dynmap users