I recently added a extra harddrive to my win 2000 pc,
after I installed it booted fine. after I formatted it now it trys to boot to that drive. I found a boot.ini file, it shows both drives in there one is 0 and the other is 1 so I changed the order to select and still the same thing, so then I change the numbers to the first drive on both options and it created another option windows 2000 (default). it trys to boot to that now grrrr.
can I just delete the boot.ini file?

Just edit boot.ini to correct the entries.

You don't need an entry in boot.ini for the second drive unless it has an operating system installed on it, and you would like the choice of booting into that OS or the other.

Assuming that the only OS you have installed is Win 2000 on the first primary partition of the primary master drive (drive "0"), a stock boot.ini like this should work:

[boot loader]
  [operating systems]
  multi(0)disk(0)rdisk(0)partition(1)\WINNT="Windows 2000" /fastdetect

does it matter if the drive(the new slave) had an OS on it before?
I formatted it to erase everything, so I could use it for storage.

If it's been formatted it doesn't matter. But make sure your jumpers are set correctly; you have two choices: you either need to set both for Cable Select (CS), or (generally preferred) set the Master drive (the drive with the OS) to Master (MA) and the Slave drive (your storage drive) set to Slave (SL).

In either configuration, the Master drive should be connected to the end of the cable, and the slave at the center connector.

If it's been formatted it doesn't matter.

Right- and because it has no operating system on it now, it needs no entry in boot.ini.