Binaries produced by GCC can be debugged in any native Atari debugger (run on Atari machine or emulator). You only have to enable debug flags during compilation ("-g" in CFLAGS and "-Wl,--traditional-format" in linker 's LDFLAGS).
After that you can load binary in your favourite debugger.
At DHS website you can find wide range of native debuggers/disassemblers.

Worth mentioning are MonST found in Devpac package, Bugaboo and Adebug Reloaded. The last one has been recently discovered after some issues with Devpac's MonST, which hanged when entering exception handler. Hopefully Adebug behaved much better and it was astonishing how many features it has. Adebug Reloaded can also be downloaded from Removers website.

Disassemblers are:
  • Desert Drain
  • TTdigger (which as far I know is the only one which supports 060 processors),
  • Easyrider

On Vincent Riviere compiler page you can also find how to debug with gdb and DDD (Data Display Debugger) remotely with Aranym(see GDB section). It wasn't tested though. This option is worth checking on Atari Falcon equipped with ethernet card, so instead of using Aranym we could use real machine. The second thing worth investigating would be debugging on remote machine via rs232 port. TODO: expand both options and describe the configuration and workflow