Start with your eyes. View the piece and look for grain direction and such. The idea is to figure out which way you need to feed the stock and if you need to chop the piece into shorter lengths or not. It's how you assess just how much stock you'll lose in the milling process.
First ... cut the pieces to rough length and width using your bandsaw or handheld circular saw or chop saw. Probably unwise to rip with anything but the bandsaw at this point in case you've got twist or something that could cause the board to kick back on other saws (table, circular, etc). Get to within an inch or two of your final length, unless your jointer or planer give you snipe - then accomodate that (if you wish). If you skip this step, you will potentially waste a lot more wood trying to remove larger flaws. A bowed board cut into smaller pieces will yield MUCH thicker final pieces compared to leaving it all one board and dimensioning it whole. You don't have to rough cut each and every piece. The limits of your tools may dictate some of this (jointer width, for example). I like to get as many same-length pieces together so I only have to mill one board to yield 3-4 pieces if possible (like rails and stiles). The biggest thing here is likely length - most boards aren't VERY far off in width, but can be incredibly out on length - both surface and edge - cup is really the only thing that happens to width and this is rarely HUGE. If it is, I pick a different board, usually. So the idea is to group together same-length pieces into a single board if you can. You can rip out final widths after it's milled pretty easily.
Second - the jointer. Joint one face straight. Don't bother caring about squareness yet, you can't be square to an irregular plane anyway. We're making the first reference face here, and it's the most important. Everything else you do will trace back to the quality of this face. Get it good and straight.
Next - I like to go to my planer and make the opposing face parallel here. This gives me two straight faces that are coplanar. This will double my feed direction options. Remember, you always want to feed the stock so you're cutting WITH the grain instead of against it. The best way I can describe this is to say you pet a cat from head to tail, not from tail to head. If you do go from tail to head, they end up with all sorts of irregular fur and the going is nowhere near as smooth. Head to tail. And think about the blades, not the direction you're moving. The direction of the blades are the important thing, there.
Now I go back to the jointer and square up one edge. If I don't have a very good edge to start with - say something that's wayyyy bowed like more than 1/4" or so, I'll take it to my bandsaw and rip a reasonably good starting edge. Otherwise it takes a bazillion passes at the jointer. Which edge do you square up??? Well that depends on the grain direction, mostly. Since you went to the planer first, you can choose either edge and have no limitations because you have two straight reference surfaces. This allows you more flexibility in more than just squaring up the edge. You can also use this to pick and choose the best grain features of the board you want to keep - say that left edge is just bland as all heck and the right edge is stunning. Joint that right edge, so your waste can be trimmed off the bland side.
Now that you have it S3S (surfaced 3 sides), you can go rip out the width of your workpieces. I like to do this on my bandsaw, too. And then i clean up the surface one last time at the jointer. Three reasons: It wastes a fraction of an inch less than the table saw does, it's safer to rip on the bandsaw anyway, and - all 4 corners are as square a as ONE tool's setup. Instead of having one edge squared up on the jointer and the other on the table saw, I only have to worry that my jointer's setup well for the milling operation. That certainly isn't required, it's just MY preference. You can absolutely rip on the table saw. Many people do.
I prefer my bandsaw for the job.
Now you can cut to final length and begin joinery.
Edit: It's NOT rocket science. But it's not a simple menu of steps, either. Wood isn't uniform or 100% predictable. The people who built beautiful furniture 200 years ago did so by intimately knowing their wood, too. Grain direction is the biggest variable. They had to accomodate it back then, too.
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