The easiest way to do it with standard AE tools, is the way Phil describes, delete the frames you want to overwrite and set it to "skip existing frames".
But if you render seqences alot, like i do, then get the BG Renderer script from
aescripts.com. With this i just set the job up in the Render Queue and launch several instances of the BG Render to overwrite the segments of the sequence, one at a time changing the workarea in/out.
Launching several aerender processes ofcourse make them each load the project, and you can get into RAM shortage or they will fight over CPU resources if it is a heavy project. But it is a workflow i use alot, since i can set at segement up to render while i keep working on another part of the timeline.
If you have fast CPUs and plenty of ram, you will love this :-)
There even is a demo version of the script that i think is full functional for a few days/weeks.