It will take Clyde a while to get used to having Bandit around. We started with one cat. Lazlo was just 8 or 10 weeks old when we rescued him. His brother, Sheldon, came in one week later. It took them all of an afternoon to get over the fighting. Their sister, Spooky came inside about six or seven months later. She was terrified, and lashed out whenever either one of them came within a few feet of her. She is pals with both of them now, but it took weeks for her to calm down - and months for them to really become hanging out, playing together pals. Any time we've had a foster kitten or adopted another cat (we adopted two subsequent to bringing Spooky in), it has taken her about six weeks each time before she really accepted them being around.
In any multi-cat household, it will take a while for the cats to accept each other. And one will have to establish dominance - and it may not end up being Clyde!
A couple of things you can do to make Clyde more accepting:
Whenever you come in, lavish him with attention first.
Do you free feed them? Or do you provide them meals? If you give them meals or treats, always give Clyde his first, then give Bandit his.
Make sure to give Clyde play-time first - although Bandit may try to play at the same time. If that happens, do you live somplace that has more than one room? Then you should take Clyde alone at least once a day and play with him exclusively for at least 10 minutes.
All of these things will help him feel more secure.
Also, height is a sign of dominance for cats. The more vertical space you can provide for them, the better. Bookshelves they can climb up easily? An entertainment center they can get up on? Or buy a cat tree (or two. Hubby and I live in an RV, and we took out the dining room and now have 3 cat trees in there. For us it's kind of a must, though, with five cats and us in here, LOL!).
Re: the litterbox. You're very lucky Bandit uses it! Often they're so used to using dirt or leaves or whatever that you have to put a layer of dirt on top before they get comfortable using the box. There are several things you can do.
1) You should provide one litterbox for each cat. (We don't have the space for that, and our cats manage to share two boxes - but I clean them a MINIMUM of two times a day, and often up to four). Cats can be REALLY picky about their litterboxes. Often if they don't cover up their business it's because the box is "too full" in their opinion. So frequent scooping could solve that problem.
2) If the box has nothing but litter in it, and Bandit still doesn't cover up his business, keep an eye on him. When he goes, as he's leaving the box, hold him gently and take his paw and scoop litter over what he just did. This has worked for others - it doesn't always work.
3) It might be smelly just because he's adjusting to a new diet that's much richer, on whole, than what he's had access to for his completel nourishment. It could take a few days or a week for his tummy to adjust, and he may have diarrhea. This is VERY common. Whenever you introduce a cat to new food, it's best done over a several day period by combining the "old" food with the new food, gradually increasing the amount of new food. Of course, you're not about to mix mice and garbage into his cat food, so you'll just have to lump it this time.
Re: scratching. You may want to consider one or two other types of things for Bandit to scratch on. Don't know if you have an "other" or ever plan to live with anyone or get married (or whatever), but your kitties can live to in excess of 20 years, so you may want to encourage proper scratching behavior so you don't have problems down the road.
Cats scratch for several reasons - and they need different types of texture for those different reasons. They like both sisal and a loose weave type fabric (like carpet), so you may want to consider a carpeted scratching post in addition to a sisal post. And cat trees that are carpeted or have both carpet and sisal are great.
I LOVED it the first time we brought home a cat tree!!! Somehow they immediately knew it was for them. They were all over it. And they stopped scratching everywhere else in the house (except the one sisal scratching post we have). They have soooo much fun running around, jumping all over them, chasing each other around... cat trees are a lot of fun for you and your cats.
Also, we found a sisal scratch pad that goes on the floor. The back is a kind of rubbery thing. One night they were so rambunctious that thing got flipped over - and it was covered in scratch marks. Turned out they liked the rubbery side better than the sisal side, LOL! Walmart sells those "puzzle piece" type things that go on the floor in a children's play room or something? The smooth side of those is the same texture. They go nuts for it. And I think they like having the "horizontal stretch" scratching option in addition to having the "vertical stretch" stuff.