I found the best way of completing the end order mission was to use the IG to build a base in the starting corner. Use the IG commander to keep calling the Landraider back to the starting corner (

WARNING

be quick as the LR will move if left alone for about 30 seconds). Keep doing this until you have built up your base and are heavily armed.
Whilst doing this build up the Eldar base as well and get to the Fire Prisms. Beware of the warning above, you will need to keep switching armies. Once you have fire prisms use them to destroy the Orc then Chaos bases along the bottom edge. Then use the tanks & IG to blaze a trail up the middle for the LR to follow. You will have to call it using the IG commander or it will go off on a tour. The use the Eldar to destroy everything along the right hand side.
When both armies are in control of the battle field save and then complete the mission with one army and play the final mission as that army. When that is done you can return and switch armies from the save point to play the final mission as the other army.
