Changing Tunes - Question

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I have the same tuner and am going to use it for the first time tomorrow. I can't think of any reason why you wouldn't be able to switch from custom to custom.

I had the Steeda CAI, tune on my car, w/SCT tuner.
I just installed the Boss intake & longtube headers, so I needed a new tune.
I got my tune emailed to me from Steeda.
Before i could load the new tune on my SCT device, I needed to return the vehicle to stock because the SCT device was married to my car.
After I loaded the new tune on the SCT, I then flashed the old Steeda 93 tune back on my car so i could drive it to the dealer for the Boss install.
After the install I could load the new tune right over the old tune.
So, I only needed to return to stock to load the tune on the SCT.
I had to call SCT support for all this cause I didnt know what I was doing. They were very helpfull, and spent a good amount of time with me on the phone.