The second generation Apple Pencil requires close-contact with compatible models of iPad to charge the Pencil. Charging through most covers is not possible.
There are several third-party manufacturers of iPad covers that permit charging with the iPad cover/case in place. Some hold the Pencil “captive” whilst docked with the iPad, whilst others rely upon the magnets to hold the Pencil. The latter types may be less suitable for some users as the Pencil can be easily dislodged - and potentially lost.
Whilst there are many to choose from, I would initially recommend that you look at Otterbox and STM - both of which have covers that can securely accommodate an Apple Pencil. Some covers from both of these manufacturers are also carried by Apple, both online and in Apple Stores.