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As far as numbering components goes, we typically will number all the components on page 1 in the 100 series, page 2 the 200 series, etc. So the first resistor on page 1 will be R100, the 2nd R101, and so on. And it is good to have the components numbered such that related ones are in the same range.

On a large design, this makes it much easier to find the right section.

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When not too constrained by size and particularly for prototyping, I tend to use short descriptive names that are not too hard to decode. For example you could use Cby* for bypass capacitors, or maybe if you have a series of LEDs, then you could have Dr, Dg, Db* depending on their color, and similarly Rr, Rg, Rb* for their respective resistors, or Rpi* for I2C pull-up resistors, etc.

Sure you could have a look a the traces to find those out, but it's not always straightforward.

This makes a big difference when debugging boards IMO. For example now if you see that your blue LED is too bright again (as is usually the case ;)), you can just look for Rb* and fix it without the schematic.

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