Hi Andy,
Goran is right on the money, try to stay clear in your mind as to exactly what your building, if, as you say, you understand that compromises must be made your already half way there mate.
As far as your A arms are concerned the uprights you go for are the variable you've no control over and are pretty much going to dictate your suspension arms lengths and chassis mounting points. Also worth considering at this point is your steering rack, if it came from the same source as the front uprights you'll save your self a lot of grief further down the line.
But back to the software, as mentioned in a similar thread, SusProg3D is good and armed with something like Alan Staniforth's `Competition Car Suspension` you'll have the information you need to fully understand what you're looking at and alter what you can within the design parameters.
Try to remember that the chassis is the last piece of the jigsaw, it's only there to hold all the bits together, as long as everything fits and it doesn't wibbly and wobbly about all over the shop (and your bits don't fall off!) it's doing it's job.
