I tend to fit the clutch/backplate and levers to the 'box and then fit the whole unit to the engine , fitting the bolts via the window underneath. If you turn the engine carefully with the bolts not fully fitted, you can turn the engine, fit the bolts and then fully tighten them as you keep rotating the engine.
If the engine blocks, back off and tighten a bit more
I usually remove/fit the engine and gearbox as a single unit because it's quick and easy, especially with an S1 engine. A little bit more difficult on S2 or Lusso where there is a double bulkhead, then it is easier to fit without the rocker cover on