Looks like you have a good handle on how to setup conversion tasks and monitor locations.
You can create a second monitor location to monitor the mce-converted folder. In the Expert Settings make sure you select the Remonitor Converted Files options, by default MCEBuddy will not monitor converted files to avoid an infinite monitoring/conversion loop, hence this option was provided for users who wanted to daisy-chain the conversions (output of one as the input of the next).
Once that is done, create a new conversion task and in the Expert Settings select your monitor location and select the second monitor location you just created. This allows for one to one mapping. Make sure you do that for the first conversion task also (like to the first monitor task).
Here is a step by step example of daisy chaining with a delay into it:
Once you’ve done that you can refer to this post for details on how to tune Comskip.