Take good care of your printout in your bed.. you know it's under age....
The structure looks like admin -> reseller -> customer -> email/ftp user . So don't confuse the terms, although in business a reseller may be a customer in your eyes. Just stick with ISPConfig's terms.
The only config panels I really know besides ISPConfig are Confixx and Plesk, so I know it can be a bit confusing at first. I don't get the point in having homedirs with ftp access for email users as well. I just don't think about it and so they do not get in my way
If I remember right Till wants to seperate that in a future version or at least add a global option to change the default behaviour.
Have a look at the ISPConfig website. You'll find a page "Download" with tools & add-ons for ISPConfig and there you'll find phpMyAdmin. The link will get displayed under "tools" in ISPConfig.
The quota stuff.. I'm not sure (after only two months with ISPConfig but having migrated more than a dozen of customers mit twice as many domains).. I only use the setting for web's and leave the single user quotas at -1 (unlimitd). I'm pretty sure that means "all the space that is available in this web", meaning that mail, database, web, log and user dirs may never accumulate to more than what you set as the web's limit.
If you want to have three sites with on admin account each, just create each site, select the site, go to "User & E-Mail", add an account, turn on the "Administrator" checkbox and you're done. You can add additional email accounts whenever you wish to.
Maybe what I refer to as web is called "site" in the English version