The tapered part of the thread, eg the part that threads into the master cylinder, requires sealant. The AN nut and flare connections such as you will find on the fuel lines will seal by their design. They should not have sealant on them.
That permatex can be a bit sticky. When I was mechanicing(?) we cleaned up with a little IPA. It's still a good sealant and will certainly do the job.
Hope this helps