Making a Smart object Box with nothing in it for a script.

Im very new to photoshop so i apologize if this is a dumb question, but I am currently using a script to make mock up designs in photoshop that essentially takes a files and fits it to a designated smart object you have set up in the mock up, however, I also am in the process of making PNG's of the same designs for the actual product I am making.  I have to res-size to a specific area,  copy, paste and mirror the design on the other side of the page and the process takes a lot out of my day for hundreds of designs. 

I am trying to speed up this process by using the same mock up script to just place the design in 2 smart object boxes that are already sized and in place instead of 1 however I cannot figure out how to make a smart object box that has transparent background and there is nothing in it considering this is not for a mockup that usually would have a background to it. I can use a white background and make the smart object that way,but when I try to "remove background" afterwards it doesnt remove the white parts on the insides of the design, creating more work. If I could just make a square box with transparent background and make that box a smart object, i could then use the script to paste all the designs into the boxes with no issue but I dont know how to do this. Ive been searching every thread i can find but not finding a fix for this. Google is telling me it is in fact possible to make a smart object with nothing in it but its not telling me HOW to do this. Also I need a solution that allows color, some of the solutions I saw told me to change the blend but it only works for all black and white designs. 

Please let me know if Im wasting my time searching and just need to tough it out, or if there is something im missing.