Will the inner sill not correct that hole - I thought they usually came to the first 'groove' in the floor pan.
will that be sufficient? i.e stop the rust spreading... ir will i need something to cover that hole then put the inner sill over the top.. i suppose it doesnt have to pass an mot so should be ok as long as i cut out as much of the rust i can..
There should only be one thickness of metal there - using the inner sill you have as a template cut out the rot and weld the inner sill in its place. You shouldn't cover holes up - cut them out to good metal and then replace (in this case with the inner sill).