I don't know of a way to do this in a single feature. You could probalby use an Extrude Cut to remove the existing wall where you want the recessed areas, then use a Sweep to add the new recessed wall and side walls. An Extrude could get you the end walls. Fillets at the end to both the inside and outside. It would probably be a good idea to do one recess, then Pattern to get the rest.
My first suggestion would be to do the cutouts before the Shell command. The Shell will take care of the inside faces.
Feel free to post the file here and we can take a look.
Yea i managed, thanks Alin and Jerry both suggestions were great