There should not be a problem having the downdraft system installed by Sears after the cook top is initially installed. I recommend that you check the installation requirements and make sure that you have the space needed to install these appliances.
Here is the installation guide for the cook top (model 790.3242 . . .):
Here is a link for the installation guide that pertains to the Kenmore 30" downdraft vent model 59960 (full model number 233.59960400) that you are likely describing in your details:
Use & Care/Installation Manual
The information in these installation guides should help you verify that you have the proper room to install both appliances.
You can call the Sears Installation Department at 1-800-605-2128 to verify that they will install these appliances separately. You can also visit the Sears Installation website at this link:
Sears Home Services -- Installation
If you need more help, reply with additional details (and the model number of the downdraft vent).