The more you lay the shocks over the more the travel is affected. Also the more you lay it over, leverage is increased and a stiff shock will become weaker in compairisn to the same shock straight up . (if that makes any sense)
example
Straight up, max movement, 1 to 1 per the axle movement.
Lay them completely horizontal (just as an extreme example) No movement.
I know you know this.
If you can match the travel of the shock with the travel of your suspension, with a little extra each direction, that would work. but the compression is the most important.
When you jack up the frame, the suspension will most likely hang from the shock. (not always though). This limit is felt when hiting a big dip and the suspension unloads completely.
The max compression should be limited with a rubber bumper, not the shock bottoming out.
Coordinate the two together, the shock travel and the suspension travel.
They do have to look right also, thats personal preference.
That is all I know.
Having seen what you have done already, I bet you have no problem figuring this out.