UPDATE 3: I learned that one way to do it is to simply make a new processor definition, it should be fairly straight forward to port already existing 68k disassemblers to the IDA SDK. Still too cumbersome in my case because I only have a single 68k project that needs analyzing. This solution will work with older IDA releases in case the free updates period has expired and one is too poor to refresh one's IDA license.
UPDATE 2: Igor Skochinsky points out that there's a bugfix. I still want to know what is the best work-around for older IDA (6.1).
UPDATE: I found that later version of IDA such as 6.8 (which I don't have access to) has a "mapaddr" command in the machine .cfg files. Don't know what mapaddr does exactly, can it multi-map addresses?
In this question: https://stackoverflow.com/questions/30987128/m68k-ida-pro-24-bit-addressing/38314561 the user had a similar problem to mine, that was never solved.
Lots of 68000 systems have 64kb of RAM mapped in two 32kb segments, FF8000-FFFFFF and 0-7FFF, so you can use word addressing to reach the entire RAM faster, because branch offsets are 15 bits+sign. This was common on other processors as well back in the day.
I split the code dump into two segments like that, however doesn't really work, because the Motorola 68k is a bit schizophrenic when it comes to addressing. Is it 16, 24 or 32 bit? It is really all at once.
IDA doesn't take this into account, meaning it won't understand instructions like this:
movea.w #$8234, a0 move.l (a0.w), d0
This should move the dword at FFFF8234 to d0. I'd like IDA to understand that $8234 is the same as $ffff8234 and use the symbols etc.
What I have done is to find every movea and lea instruction and if they are loading wrapped around addresses, I change them to a manual operand referencing the FFxxxx space.
However, while that let's me inspect the references (by clicking them) IDA doesn't really understand how the addressing works, meaning I get little other help from the environment, and subroutines and calls are not detected correctly.
For the record I am not an advanced IDA user.
Edit: for you non-68k guys, movea and lea are just move instructions that can put stuff in address registers, (almost) all addressing is with address registers a0-a7.