Polydactyl kittens & cats in New Orleans, Louisiana

I rescued her at 4 mos old from the rear of a Laundromat on a very hot day, 100°. The Laundromat mgr told me that she was dropped off by a lady who said she was "in her car and" she "didn't want her". She's got good behavior except that she's trying to rule the roost. She wants to rule over my 10 yr old fixed male house cat who's very sweet . He's raised a lot of kittens I found it adopted over the yrs (to train them for others who wanted a trained kitten ). But Honey has been peeing on the rugs all over the house to make her scent everywhere. I've tried the pherome sprays/plug ins, cat urine cleaners, catnip and treats. I let both cares outside at night and keep rear door open enough for them to come in. Honey comes in a lot to check up on me but during day when I'm at work she does her spray thing. My older car doesn't even want to come in house anymore. Im sure he's tired of her scent marking. She is very good and loving otherwise, but I think belongs in a home with no other cats.