Yes, the algorithms process the input, and that process returns the output. What order you have, is - IN COMBINATION WITH THE FX SETTINGS YOU DIAL IN - always going to have some degree of impact on the audio. The best thing you can do is to learn what the impact is, but it takes a lot of experience before you remember the result of complex chains of FXs where those FXs are in a certain order. Becoming great with effects makes you a great engineer, but it takes a lot of practicing before you get a great sound, effects often degrade the sound when they are not properly applied. For instance. Reverb before or after compression. For reverbs with long reverb time, it can sometimes work well to place a compressor after the reverb and adjust the compressor release time to a quite long release time and then feed that back into another reverb followed by another compressor. This can cause resonance between the reverb tails and can be incredibly sweet when you learn that combo well. But reverb can also be placed after the compressor, in this case you might use the compressor to do some of the job of the reverb, in order to get a more clean fx footprint, what I mean is that instead of using the reverb to enhance the size, you might do that with compressors first, then once that is dialed in, then you add the reverb on a much more dry setting than would have been required without the compressor. The difference might then be a little less cluttered air in the mix.