Intake boots

Hello everyone, just wanna know if the intake boots have a specific location?! Can I screw the Left one on right side to have the vacuum in better position or Face down for synchronization? Thank youu 

On the Z650/900/1000/1100 the manifolds are straight and can physically go in any position and orientation.
On the ones with brass vacuum ports it is only the ports position for ease of access which may determine their position.

I ordered new boots for my vm28 with brass vacuum port like the old one.. the problem is that before I had to drill the rubber bolt holes to fit correctly the boots in the head.. just remove some material in the 2 holes of the boots to center them correctly!!?  The brass are face up. But Im wondering if I install them face down if its a good idea!?

Yes! elongate each hole slightly to fit the head and keep the manifolds central to the ports.
The stock position for the brass vac tubes is facing down and outwards for easiest access but it doesn't matter which way they go so put them wherever is convenient.