Like most I start with the hull first, then I usually do a bare-bones "deck plan", mostly so I'll know where not to be running the power system.
Then I'll build the power system till I hit the soft-cap. Then, I'll rough-in the thruster system.
Next, I'll see if it can move without draining the battery. If it can't, devote space to docked reactors of some sort.
If it can, move on to a more refined interior plan, accounting for Rooms & Corridors, instead of just deck height.
(I've found it easy~est to build the corridor first, unless I have a burning need for a specific room to be in a specific place. EX Deflector control should probably be really close to the deflector)
Then comes the "fiddly bits" how much shield cap, and how much shield regen?
This part takes subjectively the longest, as it is massively influenced by:
WEAPONS. What kind, how hard will they hit, will there be more than 1 kind?
Will it be mostly Turret-based, and will I need to shove in even more docked reactors?
Finally, finish the RP grade interior, and put a USD-1 dock point somewhere.
Interspersed all through this process is "tweaks" to the exterior, and to previously completed portions.
EX: I felt compelled to re-do the detailing on the hull over 7 times on one build, before I finally got it "right".