Do I need to wait for my domain to be transfered to use my account ?

No, The account is ready to use when you receive the confirmation and setting details. You can also use the domain alias (such as login.rootr.com) to prepare the domain web site, so it's all ready when the transfer is conplete, and user browsing don't see any transition. Accounts with multiple domains have one alias for each, such as: http://example.com.login.rootr.com/
This method uses subdomains and is completely independant of html code.

How to set up mysql on my account ?

Shot an email to support to add database(s). Users with their own mysqld server (medium plans and higher) can set as many as they want on their own, as well as controling mysqladmin and similar commands.

You support both apache 1 and apache 2 ?

Victoria plan accounts and higher can have their own apache instance, which can be apache 2. Some language and interfaces still need apache 1 for full operation. We keep adding features and languages in apache 2, as they become supported. Apache 2 is already very stable and used in production environments with RootR.Net.

What is meant by independant Apache instance (IHPG) ?

With this type of setup, you have full control over Apache server, including httpd.conf, apachectl commands, http process control, and more. in fact you can even compile your own apache. You can also use other HTTP servers which are non-apache based, or possibly create your own HTTP server, which can be production necessity for some businesses. It can be also a rewarding educational activity. The indepandant apache instances run under you own user and group. This is available on Victoria plan accounts and higher. Account can use both Apache 1 and Apache 2 on different domains if they choose to.