I don't know about how the rest go about it ... but I like to "Level" the terrain down to just above the water line. Barren of all trees and hills ...
I like starting off with a clean canvas, next I create my own layout ... like sketching out what I want ...
I prefer the smallest settings for the greens and tee boxes ...
Once I have a track laid out to the distances I desire ...
trying to keep the lengths within accordance to
USGA Par length and Yardage guide for Men
PAR #3's up to 250 yards
PAR #4's 251 to 470 yards
PAR #5's 471 to 690 yards
from there, I start laying out fairways and doing initial terrain sculpting ... for each hole as I go ... I always have a plan as I go ... but never sticking to anything ... I like to let the course grow on its own ... it's a fluid process ... I use the ... "if it looks right" method ... Once I have the hole laid out I play it several times ... looking the layout over from lots of different viewpoints.
The trees and bunkers are the last bit of the process ... If the course looks and plays good barren of trees, bunkers and water, it's OK to have a few trees and ponds setup ... as to set the look you're after ... but with too much "stuff" on the course, obscures the sculpting part of the design stage (just my humble opinion).
I tend to try to keep the course looking like something that you would find on a real course ... there are a lot of those who seem to think all bunkers need to be deeply recessed in a pit. I will tell you will not find that many courses that have deep recessed bunkers on every hole, and especially 200 yards from the green ... maybe once your within 50 yards or closer ... but fairway bunkers, rarely.
Never try to have a fairway cut roll-off into a bunker, same with greens and the fringe. they shouldn't roll off steeply into a bunker.
Think like a greens-keeper or maintenance man in-charge of mowing the different cuts of fringe and rough. If it is feasible to even mow the bank your placing that first cut of rough on ... Too many course do not take this into account and thus fall into a fantasy course category (IMHO), because, no course superintendent would hire workers to hand cut the rough with weed-trimmers, in order to cut the slopes on which some have their fairways on, or 1st cut of rough ...
If it cant be done with a mower, flatten it out so it looks like you could cut it with a riding mower.
These are my personal opinions on a good course layout ... its all in the details ... but, doesn't mean its a STANDARD, and their are many who will fight my opinions on methodological course development. This is just my opinion, you can find others who have maybe even a better way to tackle the course development, but by all means, attempt designing your course with using minimal auto-generated fairways, bunkers and trees ... or you will end up with a course that looks like about 90% of the course published.
Take the time to CREATE your own course ... everything you build shape and place, is intended to be there, placed by you ... not a random generator ...
enjoy your design, and chances are someone else will too ...
Hope this helps ...