You don't need to worry about any code that Redboot may place at the exception vector. Redboot runs in polled mode, so when loading non-eCos applications there's nothing to worry about there. Preserving Redboots exception handler is only an issue when loading eCos applications.
The documentation is admitedly a little unclear on this. What it was intended to say was that the exception vector should not be placed so that it causes the downloaded code to overlap the Redboot code assigned to the "text region", "rodata region" and "rwdata region" assigned in configtool.
The simplest way to achieve this is to leave Redboot running from flash, ie. select a ROM configuration, and then allocate a small on-chip memory for Redboots "rwdata". The remaining memory can then be used for the downloaded application.
However you don't need to use seperate memories, you just have to avoid an overlap.
