Hi,
If I understand you correctly you have a custom bootloader + application and now you are trying to program it into your FRDM board, right?
Since your App + bootloader should not overlap in the flash memory you can either manually merge srecord files into a single srecord file.
Other approach is to link generated binary (e.g.bootloader) with application to create a single elf/srec.
With FRDMPK144-Q10 board you can easily program the created S-record using OpenSDA - Mass Storage Device (MSD).
Just plug the board via USB cable and EVB-S32144 removable storage should appear.
Then easily drag&drop your srecord file into this drive and it gets programmed.

RAppID Bootloader could be used but I don't quite understand why you'd need another bootloader in your project if you have a custom one already?
Hope it helps.
Stan