Orientation won't matter - no moving parts.
However, I do concur that you'll have heat trouble if you don't watch out. Get some aluminum sheet (something fairly heavy - .040" or better) and make a heat shield - just like you'd see for an underhood CAI kit.
If possible, have the heat sheld to protect the PCM, and then see about venting it somehow so it has decent air circulation as well. With solid-state electronics, heat is the enemy!