You may not have chosen the best amp for what you want to use it for. If you get an FBV Express MkII pedal, you can switch between the 4 preset channels.
Note sure why you are unable to save the clean sound you want - possibly you are not holding down the button long enough. If this doesn't work the way it should, there may be something wrong with the amp, and you'll need to bring it back to where you bought it for exchange (the 15s are not serviceable).
To get any particular sound you are looking for, you will need to experiment with the tone and gain and volume settings - the tones you get will vary, depending on what guitar you use.
I have to push the Shortboard MKII here, I can get just about any tone I need using the software and the pedal; I can also edit all the sound so that they're all clean and build up on top of them. The amp is great without the pedal if you're just messing around but you really won't be able to get the full editing capabilities without the pedal.
when you setting / editing your channel, pick the channel you want to change,
change the settings as you like, then hold down the same channel button you are using,
it will flash a few times then stop, your channel should be saved then. i'm using the S IV 75, it might be different, but i doubt it.