This is useful for a number of reasons, but just do it anyways.
You will need a copy of batch compiler, which is practically discontinued and was included in the Nazi Zombies: Portable Beta 1.1 mapping kit. You can download it here. This also works as a "portable" copy which doesn't require an installation.
You will need a copy of your map file's .map; this can be generated by saving automatically in jackhammer once you run your map, but make sure to have a recent copy.
Open your map's .rmf/.jmf file and select File -> Export Again to save your .map file.
That is all that is necessary for Jackhammer. You may close it. Open Batch Compiler.
If you are setting up Batch Compiler for the first time, you will need to go to Options -> Setup and set your CSG, VIS, RAD, BSP, WADRoot, and Output folders. WADRoot is just the folder where your .wads are contained. The others should be self explanatory given the fact that you set up Jackhammer.
The bottom bar is for you to select the path to your .map file. You may hit "remember file" for the next time if needed.
Go to the CSG tab and select "WAD auto detect" and on the right set the path to all of the .wads you used in your map. If you need to know which wads you used, then open the .log for your map (generated by jackhammer) and scroll down until you see the HLCSG section. You may alternatively search "Using Wadfile" and go immediately to it. This section will tell you all of the .wad files you have used. Set every wad you have used in the input and select the checkbox.
Select the "VIS" tab and select "FULL" and the checkbox for "Vis Type."
Lastly, make sure that you check "CSG," "VIS", "RAD", "BATCH", and "BSP" on the checkboxes to the right.
When you are finished, select "Run" and the map should compile.
Please let me know if you have any questions.