1) Install latest SAM-BA which can be downloaded from Atmel's web-site
2) Solder TEST jumper
3) Connected the module to mini USB cable
4) Wait 10 seconds
5) Disconnect the module from the mini USB cable
6) Unsolder TEST jumper
7) Connect the module to the mini USB cable again
8) When asked for drivers point to the driver folder in SAM-BA installation directories
9) Start SAM-BA
10) Choose the correct settings - COM port from device manager and at91sam7s64 controller
11) Click connect
12) Load  MOD_MMA.bin from already downloaded ZIP and program the board

There is good help file on how to install the the drivers located in the SAM-BA folder. More specifically it is located in the /doc subfolder.

If you need hex to bin converter software there are a lot of free tools available in the web. Choose the one that best suits your needs (depending on operating system, architecture, etc.)