I'm not sure exactly what you are trying to do. It sounds like what I usually do though. You can separate them into files and just compile them to a temporary bin file. After that, include the bin in Atlas or whatever assembler you use. This way you can control via code where the blocks go.

This. There are any number of reasons you'd need to be able to jump around in the ROM you're inserting to. Atlas was designed with this in mind. When you insert a second (or third, or fourth, etc) #JMP command, you'll end up with multiple "blocks" in the output, each one with its own readout and/or errors.

Most of my stuff is one or two text files, each with many, many #JMPs in them. I typically keep dialog separate from non-dialog, but otherwise...