These are easy:

It was not boiled but grilled.

It was not only boiled but also grilled.

But what should I do when I have to combine them with "should have" etc?

It should not have been boiled but grilled

It should not have only been boiled but also grilled

or

It should not have been boiled but should have been grilled

It should not have only been boiled but should have also been grilled