the memory area of pocketstation is identical to a normal memory card, so you can use any memory card reader / writer. I use MemcardRex (but you can use any). That tool you linked runs on the PS 1 itself, not convenient for me.
In pk201, you need two files: KROM (pocketstation specific image, go find it somewhere), and FROM (the 128KB memory card area, exactly the same as any other memory card, this is the raw memory dump, I think also known as .MCD, might be wrong)
MemcardRex supports just drag and drop FROM into the app, supports pretty much all formats you want, including .gme, so what you want to do is just open both FROM and the .gme and transfer it from the app