the vac/boost line from the manifold opens the wastegate at 6-7psi stock. by putting the mbc inline you are disrupting the signal to the wastegate so that it takes more than 6-7psi of boost pressure for it to open.
the reason your instructions show it there is because it is a universal mbc and some cars have the vac/boost line "T fitting" on the turbo outlet. it does not matter, you can source the vac/boost line from anywhere on the charge side (turbo compressor outlet, intercooler piping, intercooler, intake manifold etc)
sourcing it right off the turbo gives the worst spool up, but best most linear boost levels. sourcing from the intercooler is the medium setting, sourcing from the intake manifold gives fastest spool but will cause slight spiking of boost pressure.
either way the difference is so minor you would barely notice it.
if you are losing vac it is because you have done a poor job on your connections.
if you are getting more flutter then your BOV definately has a crappy vac connection.
the boost gauge, BPV and wastegate line all most be top notch vacuum line with really good connections for everything to work right.
Go buy some zipties and make sure everything is tight.
dont **** around with this stuff or you are going to be complaining about how your motor blew up driving down the street. if you dont completely understand what you are doing just put the vacuum lines back to stock and walk away.