You may not need to do anything special to accomplish what you're wanting to do. Downloading the frequencies from RR requires software (unless you're simply looking at the web site and manually programming in the frequencies), and the software is written under the design of "this is what I want my scanner's programming to be", not "I want to add this to whatever is programmed into my scanner".
The software will erase all programming and then write the new programming to the scanner so whatever you had programmed in will be gone and only the new programming will be there. To do the "add this to the programming" using software, you'll need to first download your existing programming to your software, make any changes (including downloading them from RR), and then upload the programming from the software back to the scanner.