So today my boss/manager walks in after a meeting,
"your project, its going on a rented server."
Well, not those words exactly, but the result is clear to me.

Where before it was behind a company firewall, and did not need exposure to the internet, it now needs tight security.
It needs all management available from a web interface. I had intended to remotely log on, or even put files on the server by local network/simpler means.

And what bothers me most, a bigger, more complex project and codebase...

I have picked up Netbeans, before i started on this project. It has refactoring and Git built-in and i was hoping to profit from this.
I have a decent understanding of php itself, and am trying to use a modular approach to this project to improve mantainability after launch(Classes).

Now, what i need help with, is organizing such a project. I had figured out what the actual application needs to do, now i need to add more management to it. How do i manage a larger project, is there some resource to learn from, a book to get?

Secondly, security... i THINK i have the right thoughts down from reading about security... Essentially use a peer-reviewed and well-used system. Use a salt and/or pepper in a hash in case of a DB leak. i got the phpmaster book which i believe to be great on those points.
Even so, i have never actually made a secure logon system... loooking for a resource or book here too.

I have rambled on... for too long.

Thanks in advance.