Hi Gurner,
When it comes to Logic, gain structure is something I associate with recording audio, not mixing. That's because Logic's audio channels can't distort.
It's entirely possible to have a bunch of very hot signals hitting the outputs, though, and they will distort. But rather than turning down the levels of individual audio channels, I simply turn down the level of the output (e.g., stereo output) to get signal to peak where I want it to, which is usually around -6 dBfs.
As far as FX go, and whether you're hearing more processed signal than original signal, let's look at the signal routing possibilities and you can judge for yourself -- on a plugin by plugin basis -- whether or not this is the case.
There are two signal routings you can use: series and parallel. Here I'm going to assume that you're strapping these various plugins across your 2-mix (i.e., you're inserting them in the Stereo Output channel's FX slots). If you're looking to process your entire 2-mix with, say, the vintage warmer, the typical approach is to insert it in the output channel with the intent of never hearing the original sound of the 2-mix mixed in.
Mix --> Warmer --> Output
Assuming that the mix control is set all the way to the right, so that you're only hearing the Warmer's sound, this is serial processing, meaning that the unprocessed sound is prevented from passing through it. But if you start to turn that knob to the left you'll begin to mix in the sound of the unprocessed mix. This then becomes parallel processing, as both processed and unprocessed sound are presented at the output of the Warmer.
For plugins that don't have a mix control or wet/dry balance controls, strapping them across the output channel gives you no choice but to hear the processed signal on the output.