Ideally, you take care of as many of those conflicts as you can in the composition of the song. Really good songs often don't have that much going on. It's a common thing for newbies to think that they have to have all this stuff going on, and not to consider how the parts fit together. You can have a fat guitar and a bass in the same song, as long as they aren't playing on top of each other. That's all about good composition, coming up with a song structure where instruments aren't fighting each other any more than necessary. When it's necessary, then you have to start EQ'ing things to fit (though a lot of that ideally should also fall to the performers, to adjust their tone to fit better as performed.)
The modern approach (in poppy stuff anyway) often seems to be a hundred tracks, each of them fractionally EQ'd and all layered over each other. But it doesn't have to be that way. The fewer parts there are, the fatter and juicier each of them can be, because there's more space available. And the better they are arranged to work around each other, even more so. And that kind of thing also creates movement and syncopation as well, which I think is almost always beneficial to a song.
And the sparser the composition, the more you can use ambience (reverb and delays and such) because there is space for them, and that gives your mix depth as well. That will keep the composition from sounding sparse, by filling in the gaps in a nice way. That used to be a fairly common approach, but these days it's done a lot less often seemingly.
It's definitely nothing to be embarrassed about though. If you watch lots of documentaries about artists and bands and the making of albums and such, as I do, now major artists will sometimes talk about going through all these types of issues. And a pretty common one is that failure to understand that everything can't be huge. There's only so much space and if you make one thing bigger, that makes the other things sound smaller. You have to decide what's important and what's secondary. Give the important stuff the space it wants and the secondary stuff loses.