Tim,
I still get junk mail from Bobcad after telling them for a few years to quit. I never could get Bobcad to output useful g code. Bobcad's high pressure sales team is some piece of work when it comes to pressuring you to upgrade... I guess I need to change my e-mail at work to stop getting crap from them. And Bobcad was my first bad experience with the CNC world... back when I knew nothing. Now I know more but can't remember it all. You should be able to go to the Bobcad download page for posts and get an EMC post processor. I made them do that when I first got into Bobcad. I just checked and they do have an EMC post processor for all versions. What version are you using?
www.bobcad.com/downloads/post-processors
EMC2 does use G98/99 but it might not be what the Bobcad post is using it for.
www.linuxcnc.org/docview/html/gcode_main.html#sub:G98,-G99:-Set
For normal (not artsy fartsy) stuff I'd look at using subroutines with ngcgui. I don't have a mill using EMC yet (two to convert as time allows) but have a lathe running EMC. I find for normal things I just fill in the blanks for a subroutine and I'm off and cutting. Take a peek in the Subroutines section here.
For CAM I use OneCNC, the UI is a bit clunky but outputs good (not great) g-code. Heekscad (free) seems to be making some headway and can do waterline machining and runs on Ubuntu. I've managed to get it installed but not figured it out yet.
John