Good question. Neither.
E4 is a slanted "floor" so it is certainly not 90 degrees.
Making it parallel to the front half of the plane is difficult.
What I did here, and in many other locations was to put everything in place then glue it.
Mind you that I concluded my work on this plane a few months ago so I don't remember the specific details, but it seems to me that you will have to:
1. Insert the following parts in E4: C10, C13, C15, C27, A13, A12 but don't glue them yet.
2. Note that these parts are asymmetrical - Make sure that the little holes in these parts are oriented exactly as in the manual.
3. Carefully add one A5 part (e.g. the right side) and make sure all parts are tightly inserted into both E4 and A5.
4. Place the fuselage on its (right) side and put the other A5 tightly in place.
5. If all is exactly in place - glue C10, C13, C15, C27, A13, A12 to E4 (only) while both A5 parts are still attached.
6. You can now carefully dismantle one or both A5 parts and add some glue if necessary, or continue with F7, A12, A4, C7 and other related parts.