I typically capture in 30 second spurts, but it really depends on your pixel size and scope focal length as to what time period is best to not see rotation in one of your captures.
But yeah, you'll need to get up close and personal with WinJUPOS. It's not all that time consuming once you get the hang of it, and you can usually tell whether the data is any good or not from a single sequence stack (i.e. if it's blurry, move on to the next one
)