With the portable version look for a folder labled "Data", open it, inside you will see a folder labled "UserIcons" put your ICO files in it. The ICO file has to be created using a image editing tool like Gimp. One layer will contain an image 32x32, the second layer will contain an image 24x24. Save or for Gimp, export, the ONE file as whatever.ico
This is what I did to get custom icons to work and I am using the portable version.
Hope that helps