To sound like a complete novice, of which I am as I've only made 3 cakes but am really getting into it now and have had colleagues ask to make cakes for them. I had no trouble covering my daughters Peppa Pig cake and icing was really smooth with only a small flaw which was hidden by the head. I now have to make a large 3d 5 cake. Would it be best to cover the top part of the cake with sugar paste and then cover the sides separately and do something to cover where the two join or to try and cover the whole thing at once?

Also, I've been having to make do with whatever cutlery etc I have in the house so to cut the sugarpaste I was using the wrong side of the knife so as not to get any 'teeth' marks or dragging. What would be the best tool to get to make smmoth cuts in sugar paste?

I use a pizza cutter. I don't use fondant to cover cakes so I can't help you there.

Bump!!! I don't have a lot of experience with covering 3D cakes, so I'd love to see the answer as well! If the 3D 5 cake is like your "1" cake, I'd try covering the whole thing at once. I'd smooth it in the same order I'd do a square cake: top, corners, then sides.
As for cutting the sugarpaste, I was first taught using a pizza wheel for the big cuts. Just had to make sure not to catch the cake with the side of the handle (where the wheel is joined to the handle). I've tried Wilton's fondant tools, but prefer a knife or my angled spatula.
By the way, your cakes are looking great!