This was really helpful and I got it to work, thanks a lot!
Okay for anyone else who wants to do this, this is what I did
1. Using the tool, pressed "WC3 Editor" and loaded a premade wondercard
2. Exported that using "XSE Export"
3. Opened up the script in a hex editor
4. Changed all bytes to FF and saved
5. Opened the script in XSE
6. Created a custom script which starts off with
#dynamic 0x000004
#org @start
setvirtualaddress 0x8000004
7. Compiled the script
8. Opened up the script in a hex editor
9. Typed 04 00 00 00 at that start
10. Deleted all the FF bytes at the end and saved
11. Imported the script using "XSE Import" in the tool
12. Saved the wonder card