Based on your first sentence, I'll assume you're kind of like me. Methodical.
Now, this is based on the fact that I'm very familiar with RMXP, and everything that is needed...
But, what I do is Plan. (A lot!). Start big, with the world, geography, demographics, etc.. make some sketches or notes. Then move on to the story, and as your story develops, so do the characters.
I tend to use an algorithmic approach, starting with a beginning & ending to the main story line, then continually breaking it down into finer steps / scenes / details. Some people like to write more prosaic, like writing a book from beginning to end. Either way works, as long as the outcome is a complete story, with the major plot all hashed out, sub-plots defined if not detailed, and the characters all identified & defined.
Then I go back through the story, and make lists of all the resources, features, systems, etc.. I need to support the story. Now, this is where I get a bit anal. I have a Script template (like a movie or play script) that I use to transfer the story into script format, adding direction, action, blocking, etc...
I organize it by Location (Map in RMXP), and plot (what happens in that location based on the current position in the story.) I also have a database template for RMXP created in Excel. I fill it out as I go through the story. It has sheets for all the database tabs, plus extra sheets for variables & switches,
and materials (resources).
After that's all done, I open RMXP (haven't touched it up to this point, other than for reference, or to test functionality, or try out a script.) Once in RMXP, you can create your database from the spreadsheet, start importing resources that you have, or creating them if you're artistic. (I'm not).
Creating or organizing the tilesets, etc...
Then create / download / implement all of the scripts you want, and test the hell out of them.
Then you just use your script, sketches, and database to start mapping & creating events.
If you're not completely familiar with RMXP and all of it's capabilities, then it won't hurt to spend a bit your time making little test games, reading tutorials, seeing what add-on scripts & resources are available, and generally making yourself more than just 'adept' at it. I went through a bunch of trial projects before attacking my 'pet project', just to make sure I wasn't going to miss anything once I really got going.
Of course, this is just one way, and is no more right or wrong than anyone elses.
Milestones are good, since they give you that feeling of accomplishment, and can keep you motivated.
P.S. if you want my templates, you're welcome to them.
Be Well