You can put a jack under the engine and one on the gearbox but there are a couple of problems there, first you would need to put the jack on the sump which can cause added pressure to the sump gasket and the sump itself and it can be very slippery if you have any oil leaks. Then using a jack on the gearbox makes it very difficult to split it's alright as you are removing the mounts and housing bolts but then get someone to help and just lift it off. It's very light in comparison with bigger cars, even with the 4x4 i reached through the engine bay with the box on the floor and lifted it in position whilst another helped align it. Another problem with putting a jack on the gearbox is when you do manage to split it from the engine the akward shape of the box will make it fall to the floor (trust me on this one).
One of the best ways to keep the engine in place to stop it from moving is a tool simmilar to a strut brace and goes from one wing to the other It shows it in the porter manual then once it's held and all the ancilliaries are off remove the mounts & bolts & lift off and on.
I never used any alignment tools for the plate but to be perfectly positioned you could do.