FCU like in “Flight control unit”, it seems If your next project is a FADEC, I’m suddenly very afraid.
Nobody is able to make a nontrivial schema without crossing lines, at least I can’t do it.
Cleaner? For me it’s clean enough. Beauty lies in the eye of the beholder.
The positions, it depends. If you have a signal that follows a path, let that path show on the schema, like input stage, preamplifier, filter, amplifier, output stage. I mark and label such stages on a user layer. On other applications the parts have already approximate relative positions to each other. Or, as you seem to have done, keeping functional groups together. There are no fixed rules.
The next steps might be changing all the “R” in the resistors to the values they will have.
Then annotate all the parts. Run an ERC, fix what needs to be fixed, repeat it until ERC is happy or you really understand what’s the issue and are sure it will work as intended.
Then, assign footprints (assisted by reading datasheets), export the netlist, read the netlist into PCB_new.
Now the fun part begins, turning that mess of parts into a decent PCB.