GPT vs MBR partitions

My mac mini is dual booting using rEFIt and BootCamp and it mostly works,
except that the partition table is a mess.  IIUC there are 2 tables: the GPT
one and the MBR one, where the MBR one.  Some code uses one, others uses
the other.
E.g. fdisk seems to use the MBR table, whereas parted uses the other.
The main boot code seems to use the GPT but the "legacy boot" used to start
my Debian install seems to rely on the MBR to find out where's the
boot sector.

Is there some way to bring some sanity back?  I regularly end up messing up
one or the other partition table, so it's rather frustrating.

Can I somehow throw away the MBR table?  Or as a second choice I'd settle
with throwing away the GPT table.  Any hint?


        Stefan


PS: I can't use GRUB to boot Linux and have to resort to Lilo.  It's not
    terrible, but I prefer GRUB.  It seems that the problem with GRUB might
    be related to this partition table problem.  Does anyone know more
    about it?


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