I have 2 neutered male cats one is Leo he's 1 & 1/2 and smokey is 9 years he was a outdoor cat until recently (2 weeks ago) when his brother got injured. I have 3 cat boxes and Leo has sprayed inside everyone they are all covered cat boxes but now Smokey will not go inside any of them (he used to use them until leo clearly sprayed) and keeps going anywhere he wants in the house. Ive moved the boxes to where he goes and he just moves somewhere else. I even have a uncovered box but they do not like it i assume they want privacy. The boxes are as far apart as they can be, what else should i do?
Forcing two cats that are used to sharing a large outdoor territory suddenly into a much smaller area can lead to territorial marking outside the litter box and general stressed-out behavior. It's very possible that this is at the root of the problems. The fact that he's actively avoiding boxes when they are moved to his soiled areas somewhat points to territorial insecure marking. (Leo has already 'claimed' all those boxes by spraying, so Smokey feels that he can't use them, and thus needs to set aside some potty spots of his own.)
You may have success with using stress-reducing options like feliway diffusers, more interactive playtime, and adding more high up resting places and other resources (water bowls, beds, scratching posts, etc) to reduce territory competition.
Since the cat with the litterbox issues was an outdoor cat, it may be very helpful to mix some outdoor dirt or sandy soil with the litter (preferably unscented litter), which should help him know "this is where to go". Start with about half dirt. If it solves the issues, you can start very gradually reducing the about of dirt to litter over time.
You can also try various other kids of boxes and litter. Cats are incredibly opinionated about their boxes in terms of the type of litter, the amount of litter, the amount of privacy they require, they size of box they prefer, location, etc, so you may also have some success in changing up these variables. Almost every cat prefers the box very clean, and not too close to eating or sleeping areas. There are lots of other questions which cover this in more detail.
Finally, make sure to clean any previously soiled areas WELL with an enzyme deodorizing cleaner for pets to reduce the chance of reoffending in those spots.