I print from Production Manager bypassing Flexi all the time. I find that I get crisper better color going direct into Production Manager, at least it seems that way to me. In fact I seldom print from Flexi at all unless I'm doing a contour cut. Even that I can do without printing through Flexi. Sometimes I do, sometimes I don't. Depends on the job and my mood.
You can print PDF, EPS, JPG, etc. files directly. You can't print FS files, you need to go through the Flexi Rip and Print for those. Just light off Production Manager and do File->Add Job, or use the icon on the task bar or just drag and drop the file onto the printer's setup.
But this doesn't sound like your problem. It sounds as if your printer setup is somewhat less than optimum. Either the settings in the Rip and Print or in Production Manager are not what they might be. There's so many settings and so many interactions between settings it's hard to say where to look.
One thing for sure to look at, the Ink Limits on whatever profile you're trying to use. Flexi has a real hard time using profiles in that it won't import the proper ink limits for that profile. Look and see if you ink limits aren't all set to 100. If they are, this is most likely the major part of your problem. You need to get or make a Flexi preset file for the profiles you need.