Yes you can customize your quickbooks to better suite your business. QuickBooks offers various options to customize the software according to your requirement.
For more information either speak with any ProAdvisor or you can read out the help forum articles to better understand your needs.
You'll want to start with the QuickBooks easy step interview to set up all of your company information correctly.
Once you're in, you can now customize your Chart of Accounts and set up account for online download, connect your email to QuickBooks, etc.
You can check out this helpful video tutorials and QuickBooks FAQs for your reference:
If you can be more specific of what you're trying to customize, then I can be of help. Just leave a comment anytime.