I work with Logic Audio 4.7 because there are more possibilities to visualize the arrangement on 2 19" monitors than on a small display.
Fruity loops is a small beat box, and cannot be compared with a real sequencer like logic, rm1x or
the Akai mpc's. With fruity loops you mainly control one single instrument - the drum. With a real sequencer, you arrange the whole track. But this additional dimmension have to be controled by you, thus means a real sequencer is much more powerfull but also more complex and harder to handle. This has its impact on the whole handling by using a 'second layer' in the way you thinking.
You can treat fruityloops as an instrument for programming drums, but a sequencer USES INSTRUMENTS to perform something. This means, the instrument is one thing, how to use it (which note to play, how to route,...) is another thing.
For Example: To do the same thing like fruity, you have to use a sampler which have to be filled with all the drum samples you need (this can also be a software sampler). Then you have to go to the sequencer and play the note that is assigned to the drum sample you like. Therefor this is more work to get the same result, BUT: If you are able to use your drums WAY DIFFERENT as they appear originally by ie playing them at different tone hights, the result is much better.
I'm usually not using fixed GM drums, cause they mostly don't fit the song. In the real world, you have to tune your drum, and so this is with drum samples.
Each tom, ride, ... has a tone that should fit to the gamut you use, and i think there is no way to do this in fruity loops.