Manta is associated with the Isrotel hotel called "Yam Suf". They are a larger well funded dive center, so they have good facilities in good condition. Also their rental equipment is in better shape than some of the other shops. They schedule 4 guided dives a day, so its easy to dive as much as you want. I believe that the other shops have 2 or 3 guided dives a day. Of course any of them can do a private dive for you, but that starts to get a little expensive. I used to use them, before I started diving mostly doubles. Currently, I'm a member of Deep Siam, which is across the street, as they have both tech and rec facilities.
I agree about scheduling yourself onto one of the boats that goes out to Japanese Gardens. Since its difficult to get to that part of the coral reef from shore on a single tank, that area tends to be in better condition than some others. The wrecks that a guided dive will take you to in Eilat are sanitized boats that were sank for the purpose of recreational diving. If you are really into real wrecks, they might be a disappointment. That being said, I visit them regularly, though my first love is the coral and the little beings that inhabit it.
There are many many dive shops lining the road which gives access to the Coral Reserve. Most of them are good operations. Some larger than others, some a little better organized than others.
Note that it is law in Israel that you must show your C card, and they generally keep it at the desk while you dive. Also, if you can't show a log that you have dove in the last 6 months, they will make you take a refresher. And finally, dive insurance is mandatory. If you don't have, you can buy it from any of the dive centers.