I'm using Jaksta on two mac's. Is there a way for me to merge the contents of the two files? And is there a way to have both computers save to the same file, be it on Dropbox or iCloud or some other way?
There is no method within Jaksta itself to have a communal storage location/file repository.
In theory, If you set both programs to send downloads and converted files to a shared folder (Dropbox, public folder etc.), then you should have all the files combined and accessible within there. But each program of Jaksta will still only be able to handle files that belonged to it originally.