First yes you can setup 2 instances of mcebuddy to run in the same machine though you will need to manually configure it. Refer the documentation on how to do it.
Second you can create 3 tasks and set priorities to each task so that wtv has higher priority in the queue.
Then set the overall process priority from the main status screen to low. This will ensure it doesn't burn your CPU. What I also do is under expert settings I select only 1 CPU so yacht it further reduces the impact. That should work pretty good for you.
Scheduling cannot be done at the conversion task level. The current architecture does not support it.