You can use an application called Hexmate to do this. I think it was created by Microchip a while ago, but you can certainly use it with hex files for other micros. You can find it here: http://www.schmalzhaus.com/Tools/HexmateInstructions.html
The manual is part of the PICC18 manual which can be found here (look at section 5.15): http://ww1.microchip.com/downloads/en/DeviceDoc/manual_STD952.pdf
The command to merge two files, one called "bootload.hex" and one called "mainline.hex" and output them to a file called "merged.hex" is:
hexmate bootload.hex mainline.hex -omerged.hex
Make sure that all 3 files are in the same directory when you execute that line.