One of the advantages of PDMS is that it allows to replicate very small features, so if you just pour uncured PDMS onto the silicon wafer, it will most probably fill every nook and cranny in your device. Do you need a very strong bonding? Cured PDMS has reversible bonding to most materials, i.e. it sticks to them but can be unpeeled rather easily. If plasma is not working, you can try corona discharge. If you won't do high pressure applications, you can try to reduce the amount of curing agent-to-base ratio to get a stickier PDMS.

for bonding pdms to your silicon, you need to make sure the pdms is super clean, I would wash it in acetone the isopropanol and i usually make sure there are no particles by used tape. you also need to make sure the surface you use us super flat,

fianlly, you need to optimize the plasma time and need to leave the bonded parts over night for them to seal.

80W air plasma treatment with silicon substrate 4.5min and 0.5min with PDMS. The irreversible bonding occurs right after 15min in 85 degree oven. 

The uncuring PDMS may soak the 5um channel after 1 hour in vacuum chamber.