The Resource Kit is Cobalt Strike's means to change the HTA, PowerShell, Python, VBA, and VBS script templates Cobalt Strike uses in its workflows. Again, the Resource Kit is available to licensed users in the Cobalt Strike arsenal. Go to Help -> Arsenal to download the Resource Kit.
The README.txt included with the Resource Kit documents the included scripts and which features use them. To evade a product, consider changing strings or behaviors in these scripts.
To make Cobalt Strike use your script templates over the built-in script templates, load the resources.cna script included with the Resource Kit.