trouble formatting drives

i have an HP Pavilion 540n that im trying to get going again, about 4-5 months ago i was having problems (i think adware) i couldnt get it to work or even turn on. i had no boot disk or anything. so i bought a new HP. but now im trying to get the old one to work, so i hooked up another drive to it and installed XP professional SP2. it installed on my added drive and not the main one so now when i turn it on it gives me the option of which OS to start with (the one with pro or home) so i turn off my comp unplug the added drive and turn it on it still takes me to the menu so i can choose which OS and i go onto my old OS and i install XP again. it didnt format my drive it just updated it. i still have 11 GB left from 30 GB. ive installed it about 5-6 times and it still wont format. ive tried going onto the added drive's OS and tried to run the comand: format c: , but that doesnt work. is there anyway i can format my drive or get both of my drives to work under 1 OS so i dont have to go to the menu every time i turn it on?