You have to write a special USB driver for the phone first to get flashing working.
One that recognises the phone during that press-c-plug-cable sequence and does the right thing after that. (i.e. send the "open sesame" bytes)

For working with at commands, just use the rfcomm facility of the bluetooth subsystem and
connect your minicom terminal program to /dev/rfcomm0. The at commands are documented on se site somewhere (pdf). Also you can just type at* to see a list of supported commands. Most of them are undocumented :(