It all depends on the way the fish feed but generally it wouldn't matter which hook you put which bait on.
The 2 hooks are in any case within 30cm of one another and at 100m the angle of the line off the bottom wouldn't make one hook higher in the water than the other.
It is however easier to determine which type of bait the fish is taking if you make a routine of ie
1. Floatie on top hook Dough on Bottom hook or
2. Floatie Dough top hook, floatie bottom hook
3. Dough top hook and worm with backing bottom hook
You'll be able to soon pick up which bait is favoured by just checking which hook the fish is caught on.
90% of the time, if you for example switch the dough from bottom to top hook the fish will then take the top hook indicating they are eating the dough and a bait on the ground.