Mix custom pages with WP tools?

Hi everyone,

I apologize if this isn’t the correct place for asking this, but I’m wondering if anyone can help point me in the right direction. I’d like to build my website mostly by hand (HTML5/CSS3), but there are some database-y things I’d rather not reinvent (a login or file management system, for instance). I’m still getting a feel for the different things WordPress has to offer. Is it possible for me to build my own pages using WP tools where I see fit, or would I have to use someone’s theme as a template and customize it? If the latter, is it practical to juggle between my own and WP pages throughout a website?

Thank you for taking the time to help out a noob,
Jeff