Let's take an example: Our website is called domain.com. We have a general brand appearance at www.domain.com, a blog at blog.domain.com and a shop at shop.domain.com.
If you create a project with domain.com, we will track everything that is happening on the SERP for your domain. So it doesn't matter if your main website, your blog or your shop is ranking. Taking an example keyword like "buy domains product" your shop.domain.com likely ranks. In your project you would be able to find this ranking.
If you create a project with www.domain.com, we will only track rankings from your main website, ignoring your blog and shop rankings. In this project you wouldn't find a ranking for "buy domains product".
Our recommendation is to create a project with your root domain (domain.com) without any subdomain (www., blog., shop., etc.). You can still add your subdomains as benchmarks to your project to analyze them individually.