No need for custom brackets, that's what the mighty mounts are for: to attach any Yakima stuff to the OEM Yakima roof rack (that's what we have). Depending on what you're attaching, you'll need either horizontal of vertical mighty mounts, check Yakima site for more details, ether way they are below $30 for all 4.
There's plenty more info on this both here on club.vmag. Here's my resent post on attaching a bike rack, may help as well.