You say the manual is confusing. I cannot believe it - maybe you can give it one more try.

Well the beauty of FlashMagic is you hardly need to make any settings - just enter the Com port that you are using; Select 9600 Baud to start ; Select the chip that have on the target board; Enter the crystal frequency; And just select the block of Flash that you need to erase; ( no need to erase the whole chip - it takes time )
Browse and select your Hex file; Unselect all security bits; hit the Start button. Thats it.

Dont tamper with security bits, Boot vector etc - atleast not until you get to know more about them.

I think my steps are more confusing as compared to the Manual !

Cheers

raghu