Yes, it's quite common to just run have the pixel script, then track the results in your Facebook business account.
The pixel is just a piece of code that sets cookies and gathers data for tracking your marketing performance.
You should be able to change it at Online Store > Preferences. If not, you can always just add the pixel code to your theme.liquid file, and also in Settings > Checkout > Additional scripts . That will make the script load on all pages of your website.