concerning the annotations and using them on a desktop, the way this has been solved for the DR's with the latest firmware was through a port of xournal, so I guess a solution would be a similar port of xournal for the boox than the one you can find here
https://www.mobileread.com/forums/showthread.php?t=87593
https://bitbucket.org/mackx/xournal-dr
since the Onyx sources are public, this should be possible ....