If Malware went into the Omnitrix would he be able to control Ben, or just the Omnitrix? If he would control Ben, this would be possible by accsesing Ben's DNA and track the DNA all the way to the brain. If Malware were to just control the Omnitrix, would he control the aliens, resulting in controlling Ben?
No. If Malware retains the natural ability to possess any technology, he will only control the Omnitrix, not the person that was wielding it. Now, if Malware is part Ectonurite, then yes, he can possess both Ben and the Omnitrix at the same time.