How can you check to make sure you server is safe? Are there online tools to ensure you are free of security risks?
I don' t check anything out. All my hosting is managed so I depend on them to keep things secure. I probably should hire someone to try and penetrate my server and see what needs to be patched up before a hacker does it.
My server is also managed so I don't have to worry about this. You should get a host that is managed so you don't have to worry much about the security of your server.
I get my hosting from a friend that bought his own servers. He is smart, but I was the first person to have a website hosted on the server. He is still setting tons of stuff up, and I've corrected about 5-10 things he hadn't done yet. Things like, when I open my website in FileZilla, if I repeatedly press the parent directory button (...), I could see all directories, including all of his. I didn't have permission to view them, but I could see them. He always fixes things as soon as I tell him, but it has me iffy. I need things to be perfect when my forum gets officially launched (soon).
The best thing to do if you are concerned about security & server management, etc. if you have no idea what to do is to go to a fully managed host or pay someone to do the management for you. If you've got a cPanel server, the ConfigServer Security & Firewall WHM module is a great tool to start using to help identify possible security issues, etc.