You cannot use more than one sheet with Autocrat, so the best work-around as you allude to is to aggregate the data in one sheet. There is a way of doing this while also preserving the integrity of your data: the function
importrange. See the Google help page on it here.
With this function, you can import data from one sheet or many sheets into one "master" sheet and preserve a live link, so to speak. Once the connection is established, you will see nearly live updates in the destination sheet after a change is made in a source sheet.
Two things to note before using it:
You must be the owner of any/all sheets you want to use as source documents in your
importrange function as you have to request access to that data.
You may need to refresh the page once or twice to get your data to load the first time. However, once it does load successfully, you should see that connection in pretty close to real time.
You can then run Autocrat from the one sheet that is acting as the destination of all your source data.