The purpose of the cover panels is to finish the exposed end of the kitchen cupboards and to match them with the doors that you have chosen.
If you do not use them
IMHO
it will look like you forgot to fit them!
You need them on every exposed end or side. This means the end of a run, both sides of a tall cupboard where it meets standard sized cupboards (or stands alone) and where you have a shorter cupboard, e.g. for an extractor.
Remember also that where you have an end panel on a wall cupboard you also need one on the corresponding base cupboard and vice versa. If you do not do this the cupboards will not line up and will either look odd at the end or leave you with a gap when you try and attach them to a tall cupboard.