Making changes to new blog template theme

Can I get some advise on how to best approach the New Blogs Template setup?

I created a new template and picked a theme form the Farms 133 Themes Pack and made some changes to css, footer and header php, etc. and made it default but when I create a new site will these changes cause any conflicts with some of these themes?

I would imagine that's the idea behind the template is to customize it to your needs but I am curious to know if there are any issues before proceeding.

Any tips, advise, etc. appreciated.