No worries! Welcome to the forum.
Let’s say one image type is called Stain1 and the other is Stain2 and you have lots of pairs of each that you want to subtract.
In the Names And Types module, you use rules to select all the filenames for Stain1 (like, maybe all those files have “w1.tif” as their ending) images and assign them the name “Stain1” and then you add another rule to select all the filenames for Stain2 images and assign them the name “Stain2”.
Now you are all set to set up ImageMath to subtract Stain2 images from Stain 1! And when you run the pipeline it will run it on all pairs of images. Hope that helps!