Once the debug agent is running, and you've established connectivity between the host and the target, you can use the debugger to upload the executable to the target, and then run and interact with it.
When the debug agent is connected to the host debugger, you can transfer files between the host and target systems. Note that this is a general-purpose file transfer facility—it's not limited to transferring only executables to the target.
In order for QNX Neutrino to execute a program on the target, the program must be available for loading from some type of filesystem. This means that when you transfer executables to the target, you must write them to a filesystem. Even if you don't have a conventional filesystem on your target, there's a writable “filesystem” present under QNX Neutrino—the /dev/shmem filesystem. This serves as a convenient RAM-disk for uploading the executables to.