Marilyn is right, it really is something you just need to start using and get used to.
A good place to start would be this thread here
http://www.ipadforums.net/jailbreak-applications-tweaks/25824-ultimate-list-jailbreak-tweaks.html
It's our official unofficial "must have" list and has a lot of really cool stuff in there for you to try out and at the same time really get a handle on Cydia as well as understanding different tweaks and such.
I also have a three pieces of advice...
1) ALWAYS read the description provided for a tweak. This includes making sure it is compatible with your version of iOS. Know what it does so you can be sure it won't conflict with other tweaks. Don't just download everything willy-nilly, treat it as you would a computer and use discretion in what you download. There are a few scam apps out there. I use a tweak called 'protect my privacy' that submits spoof information for apps you're unsure about and acts as an extra layer of security for your identity.
2) Have a back up method for triggering safe mode, especially this soon after the 5.1.1 jailbreak release, as some tweaks may malfunction or be incompatible with the new update. See this thread here
http://www.ipadforums.net/jailbreak...-use-safe-mode-maintain-stable-jailbreak.html have at least 1 other way besides substrate to trigger safe mode.
3) I'd advise you to stay from theming for the next couple weeks since this is the first time the iPad 3 has been jailbroken. The iPad's large retina display makes all current themes look distorted or downright broken. This means I'd advise waiting to use apps like Winterboard as well.
I'm sure there is more but this is the most important things I think you should know.
I'm sure Marilyn would also advise you to stay away from RetinaPad as well.