First, before anything else, take a backup of your important data. This is what you would do anyway; if the data is important, you make sure it's safe even if your systems fail. After that you can start playing around without bigger fears.
Second, I'm not sure what you mean by "make a logic partitions to be a primary"..do you perhaps mean moving the partitions or something? In that case somebody else hopefully has better information..but I wouldn't go there. I would simply back up the data, then create a new partition table - yes, wipe everything out, creating new partitions and formatting them (possibly during the installation of the operating systems). It's not that big a deal if you make good backups, and if you don't, it's your loss - you really should.
I don't get - why would BSD want to be in the primary partition? Any sane explanations?
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