Here's a run down of the steps involved to make the transformation to an EFILive modified PCM Operating System (O.S).

First thing, all custom O.S's have NO calibrations in them simply because it would be near impossible for us to cover all possibilities of what might be needed to be flashed in on a vehicle by vehicle basis. So these are the steps that need to be taken.
This is based on a scenario that you are not doing a year or total O.S change.....i.e 1999 to 2001 etc.
Think of this as though you had a 2001 Camaro and you were upgrading that to one of our O.S's to suit a 2001 vehicle.

Step1 -
Read the existing tune in the PCM (or at least have a copy on hand if previously read), take note of the GM Operating System number.
The files that we currently have modified are -

GM O.S = EFILive O.S
2001 Programs
12202088 = 01250001
92111922 = 01250001
12208322 = 01270001
12225074 = 01290001

2002 Programs
12209203 = 02010001
12212156 = 02020001
12221588 = 02030001
12593358 = 02040001

2003 Programs
12579405 = 03150001
12593058 = 03190001

2004 Programs
12585950 = 04072901
12587603 = 04073001
12592425 = 04073101
12587604 = 04110001
12592433 = 04140001

2005 Programs
12592618 = 05120001

Step2 -
Find your matching O.S number in the above list and load the EFILive .tun file.
Do a full flash of this O.S into the PCM.
Once finished, the PCM will be left in a no start state, this is where you need to flash just the calibrations in from your original GM O.S.

Step3 -
Load your old tun file from the original O.S and just flash the calibrations in.
Once this completes the PCM will be in a state where it could start and run the engine, but don't get too excited just yet, there is a few more steps.

Step4 -
Read the PCM again, why?.
This will now read the modified O.S with your calibrations.
Once done you can save that .tun file as the new base file for the vehicle.

Step5 -
Important!!
Looking at your new .tun file checkout the values in the "EFILive Custom Calibrations" section and confirm they look 'sane'.
The reason for this is GM sometimes fill blank areas of the flash chip with either '0' or '1' which alters the default setting the new parameters will be set to.
I suggest setting the new parameters like so (for now) -
A0000 = Disabled
A0001 = 100%
A0002 = 100%
For further info on these, see this thread -
http://www.efilive.com/forum/viewtopic.php?t=1653

It would be a good idea to reflash your new .tun file again after it has been saved (even if you made no changes here) to ensure EFILive corrects the values in the PCM that are used by A0000 - A0002.

If you are upgrading a 1999 or 2000 O.S to a 2001+ O.S then you will not be able to use any existing .tun file you may have for your 1999/2000 vehicle.
You will need to obtain a stock (or modified) .bin or .tun file to suit your vehicle.

ATTN Beta testers - Any previous versions of 01250001, 01270001 & 01290001 will not be compatible with the .cal files that can be downloaded with these O.S's. contact me ross@efilive.com for further info on this.

Next in the pipeline for this set of mods is th 2002 F-body and C5 O.S's.
These should be ready for download within a few days.

At this stage I would encourage all 1999/2000 vehicle owners to upgrade to a 2001+ O.S, we just cannot implement some of the features we have planned into the 1999/2000 O.S's, so at some stage you folks might feel you are missing out.

Here also is some links for .tun and .bin files that might come in handy -
http://stealthv.nitro-nights.com/tunes.htm
http://www.horist.com/hptuner/

Cheers,
Ross