Ah, I think I understand what you're trying to do.
"Transparent" isn't a colour to select in PICO-8 (it defaults to treating black as transparent, but you can modify that with PALT), and the FILLP function allows you to set part of the pattern to transparent (regardless of colour) using additional binary bits. Using the previous example, you could call FILLP(0x8421 + 0b.1) and it will render transparent where the yellow is. There's more detail on this feature in the PICO-8 user manual here.
I assume when you're using the special characters shift-e and shift-b, it's using a pattern that already has that bit set, but if you want to use custom patterns you can add 0b.1 to any pattern you create.