Contrary to what others said, this not related to scenes - at least as you described.
If you load a particular amp into Channel A, it's only in A and has no effect on other channels.
Although, it has been discussed before that what settings are on "unused" channels may be indeterminate until you change them so it might appear that way... Possibly if you start with a blank preset and load an Amp block it might populate all channels with the model you select first. But I've never experienced what you described.
Now it does sound like you want to use different scenes for this, so load the 1st amp on Channel A and the 2nd on Channel B, then in each scene select whichever channel you want active. There's no need to save before loading something into another channel.