The Autopilot profile we create under inTune blade (Home > Microsoft Intune > Device enrollment - Windows enrollment > Windows Autopilot deployment profiles) don't appear under the Microsoft store for business portal and vice versa. How are they related? Which one should we use?
go for Intune if you use Intune for management. You can leverage the automated device gathering via dynamic AAD device group and automatic assignment of the Autopilot profile, that't the way to go. All extended functionality (announced at Ignite) will appear in the Intune section as well, like gathering devices not registered with Autopilot automatically.
The Microsoft Store for Business is one way of multiple ways to deal with Autopilot but as long as you have Intune I would not use this portal to do so. There is also the Partner Portal to manage Autopilot. All have different targets for management. The Store for Business can be used as a customer without Intune for example.