Does the use of a turbocharger decrease fuel economy?
In my application, yes. But only because the turbo boost is so damn addicting! I find that my foot gets heavier than normal in order to achieve maximum boost in each gear. Common sense tells us that more acceleration = more fuel consumption. This answer provides more detail on the above subject: Does accelerating faster worsen fuel efficiency?
So the short answer is; it depends. Your fuel consumption will vary according to the size of the turbo, size of the engine, level of acceleration, aerodynamic drag, and the list goes on.
Without getting too detailed about the inner workings of a turbo, it's basic function is to provide on-demand power to the engine by forcing more air (and thus, more fuel) into the combustion chamber. The key here is on-demand; instead of providing constant consumption of fuel like naturally aspirated engines, turbos can actually be seen as a fuel saving tool.
How can I limit the use of the turbocharger as to improve fuel economy?
Every turbo has a boost threshold, which is the the period at which the turbo starts producing usable boost. This usable boost is affected by the rate of flow of the exhaust gases, which is what is needed for the turbo to spool up. This limits the turbo boost at a particular rpm, which is referred to as boost threshold rpm.
So, you are correct in thinking that less acceleration = less boost produced by the turbo. The turbo isn't receiving enough exhaust gas (created by acceleration) to create usable boost. Once you discover what your boost threshold is (which is based on your vehicle and other factors listed above), you can then determine the optimal rpm's to shift at in order to stay below the boost threshold rpm.