How does Aphex Twin (and other abstract sound and beat makers; Autechre, Radiohead, etc) get the artistic control needed to create his sounds? Ive played with everything from Logic to Reason to Absynth to Battery and all seem to have good things that I like. But I'm missing the piece to put them all together. Im imagining being able to start with a base sound or sample that I have either made or taken from a loop disc or somthing, put it into a program where I can have total control over what that sound does (crackles, hisses, pops, echo's), and then send it back out to another program to be sequenced and edited into a song with other sequences. So far I have found good, easy to understand, sequencers and loop machines in Reason. I have found good sound sulpting options in Absynth and Battery. But I lack the ability to put them all together. If I understand programs like Logic and Pro Tools correctly, then they are supposed to act as a sort of "Base" station for me to plug everything else into. But all the external programs, such as the ones I previously mentioned, come from different companies and have different plugin formats (i.e. VST and AU). When I start trying to use VST converters and such, things start to get messy and unreliable.
Bottom line: When I hear an digital noise in a song, it dosn't sound like its been taken from a loop CD or any other preloaded source. It sounds as if the Artist has sculpted the sound from the ground up and then sequenced it how he/she wanted. I want this ability.
Thanks a lot for reading this far. Any help would be much appreciated.

Ideas without a means.
jeffrey