Yeah, basically it means you're screwed. It's not the reason you were hacked, it's the consequence of being hacked. You'll need to find the original hole, plug it, remove the shells, remove the modifications, and take other steps to clean up. All of the information you need is available in these forums or online. It's not a simple task and it can be time consuming and ineffective if you don't know what you are doing. sXi is generously donating his time by building a scanner to detect and mitigate intrusions, but it's not finished yet. It's volunteer work which should be appreciated and not demanded.
I'd recommend that you either educate yourself using the wiki, forum search function, and google or enlist the help of someone who knows what s/he is doing. I don't mean this to come across as harsh, but there's no simple one-step thing that will magically make everything right again. It takes time and knowledge and, if you take the time to look through some of the related threads, it takes even more time for those who have some knowledge to a) convince those that don't that they ought to be paying attention and b) teach those people how to actually help themselves.