@Bif,
First off if it already has not been done, allow me to welcome you to the Amiga.org forums. It is always good to see Amiga users with programming experience/talent return to the Amiga community, as we are woefully short on competent programmers (at least compared to the number of Amiga programmers there once were).
I can't answer the technical side of your questions, but you should be able to find previous forum threads that discuss multiple cores/multiple threading support, if not here at a.org I know I saw such a thread over at MorphZone.org not too long ago, but I do not remember the details of the discussion. It would be great to see someone with lots of experience in multiple core/multiple threading software design take a look at the difficulties in implementing such support within AmigaOS4.x/MorphOS2.x/AROS. Perhaps such an experienced person could come up with some new ideas to overcome the obstacles and figure out a way to take advantage of a second core in some way that would speed up the above mentioned OS'es and/or any newly written programs that run on those OS'es that could use the new ideas. The proposed multiple core support planned for AmigaOS4.x is just on the wish list, or their "Road Map" and there is no target date for when (or if) it will be completed, or even if work on implementing it has been started.
Lastly, even if it proves to be impossible, or impractical to implement support for multiple core CPU's within AmigaOS4.x/MorphOS2.x/AROS, I hope that you will find the time to do some other Amiga programming in the future and that what ever code you do write will be able to be compiled for all three OS'es mentioned above. One easy way to accomplish this is to use Hollywood4.5, or just about any C/C++ compiler to write your programs. Hollywood comes with built-in support to compile for multiple OS'es, including MacOSX and Windows in addition to AmigaOS3.x, AmigaOS4.x and MorphOS2.x (I would have to look at the documentation again to see if it supports AROS and/or Linux). Although Hollywood and Hollywood Designer are not "Low Level" programming languages, I have read that some very good programs have been written using them and that is where I am trying to concentrate my learning to program time. From there I will probably try to learn C/C++ next.