Just things from my experience -
i) Use the perl scripts from Club Raptor / Asameshi's site as much as possible. Especially DNM File Builder (dnmbuild.pl). It will make your life much easier, as it has built in line counting, drag and drop reordering of parts, right-click context menu to call other perl scripts, and much more.
ii) Organize the DNM file. I always keep all the parts in a DNM file in roughly this order:
1. Main body - fuselage and other extra parts (e.g. antennas), cockpit (those that needs to be included in the main model and not the cockpit file).
2. Moving parts - ailerons, elevators, rudders, flaps, etc.
3. Landing gear parts - all the wheels, struts, doors, and the interior of the landing gear bays.
4. Extra parts like pylons, external fuel tanks (you might have separate versions of the model, one with and one without external tanks).
5. Standard markings - markings (i.e. stencils) that are used for most versions of the paint schemes, like roundels and "USAF" wordmarks.
6. Individual specific markings - special markings that are more specific to a particular paint job, such as unit badges.
7. Transparent parts - All transparent parts should go LAST in the DNM file, because of the way YS graphics engine works. This is like turning on the YS flight option "reduce peep hole", but why rely on just one function in YSflight to get things displayed correctly when you can have the option built right into the DNM itself?
iii) Name your parts logically. E.g. why use parts name like "flaps-1.srf", "flaps-2.srf", "flaps-3.srf", when you can name them something more descriptive like "flaps_inboard_left.srf", "flaps_outboard_left.srf", etc. This also prevents other modders from putting a curse on your name because they have a hard time figuring out which is which when they want to do a repaint of your work.
iv) Learn both gepolyx and gepolyo (don't bother with the original gepoly from Soji's winutils). Remember some of their more important differences:
1. Gepolyx saves all vertices coordinates in three decimal places, but only displays two decimal places. This can make your life difficult if you are not careful. You CAN enter three decimal places when you manually enter the coordinate of a vertices, but gepolyx always rounds it to the nearest two decimal places when displaying it - 0.251 and 0.249 will both be displayed as 0.25. GepolyO can use - and display - as many decimal places as you specify in the Settings->Set Precision option.
2. Gepolyo can read and write SRF with either 15 bit or 24 bit color coding, but gepolyx can only accept the 15 bit coding.
3. Gepolyx always create new vertices as "rounded", and have no option to toggle the round/square status of individual vertex except the "Round All" option. Gepolyo always create new vertices as "Squared" but can toggle them individually.
4. Gepolyx will crash if you use the Set Normal function more than 3 or 4 times. Gepolyo has no such bug.
5. Gepolyo can render in openGL and you can see the model as it is in YSflight itself, but sometimes the shading/highlight can make judging the actual color difficult. Gepolyx can only display in non-openGL, but it has a Solid View option which renders the model with out any lighting and shading, which will display all the polygons in their actual color and is very useful when painting.
v) Avoid painting a polygon with (0,0,0) as black unless the polygon represents not an actual surface, but an opening like the exhaust pipe (assuming you are not modeling the inside of the exhaust) or the opening of an auxiliary air intake. Depends on the surface, I often use (16,16,16) or (32,32,32) as black, YSflight cannot do any kind of shading on a (0,0,0) polygon, while a small grey value can give something the YS GFX engine to work with. A 3D shape painted entirely in (0,0,0) will look like a shadow while a shape painted in (16,16,16) will at least have a bit of shading on it and appear three dimensional. Generally, a glossy black surface in real life will usually appears darker - or "blacker" if you prefer - than a flat or satin surface.