You will want the latest firmware, which is version 1.08. Install it by unzipping it to the card.
Then you will want "3in1 Expansion Pack Tool V1.8". To use it to use rumble in a ds game, simple run it like any other ds game, *making sure soft reset is on*.
Press "L" or "R" untill the option to enable rumble appears. Select it and push "A". The system should soft reset, sending you back to the R4 interface. Use it to start the Rumble enabled DS game.
Do the exact same thing, but choose the "ram expansion" in order to use the Browser (or any other ROM that wants the RAM pack).
For GBA games:
As Destructobot posted, you want the EZ4 client. You use this to patch the games that use flash or EEPROM for save types. SRAM save types do not need to be patched. You run the games with the "3in1 Expansion Pack Tool".
For full instructions on the "3in1 Expansion Pack Tool" simply read the post Destructobot linked to.
If you have further questions please ask.