I`d say make it as unique as possible. I usually do a low density ambient pop zone that is system wide, with other pop zones around the bases and jump things.
Patrols should be added so that pirates have an idea where to go to jumpholes and makes finding or avoiding the bases easier.
What kind of system is it going to be? If it is both Kusari and Bretonian will both police forces be patrolling?
If it has bases, what kind of commodities will be sold, how would that affect trade with nearby systems?
That kind of thing.. I find it easiest to just add the basics then start playtesting.

I see. I go for a medium-density ambient pop zone that stretches to near the boundaries of the system. I haven't tried patrols yet, and I'm told that they can crash the system. I'll look at the tutorial to see if there is anything on patrols, but just in case there isn't, anyone got any advice for making them? Last time I tried, I screwed up royally, and then the system got messed up.
About making the system unique: I'll try. Currently, I have one planet (you can land on it) called Planet Choshi. (I'll make it clear right now that Kusari is the dominant government in the system.) It has rings, just for the sake of sightseeing. I also added a battleship. I'll be putting a gas giant or two and a few space stations, most likely owned by Kishiro/Samura and BMM. I'll be hiding jumpholes to certain systems of interest to pirates and others, such as Omicron Alpha and Omicron Gamma, as well as to Shikoku and Cambridge (not to obvious places where they're easy to find, like in New York). As for commodities, well... There is one large ice cloud in the southern region of the system, and I am planning to add a medium-sized asteroid field in the northwest part. Count on the cheapest commodity being hydrocarbons, followed by optical chips and maybe optronics. And then, of course, there's the basics: Food, water, oxygen, etc. There will be a Cryer base there too. I'm not sure how it would affect trade: Haven't thought about that very much. And yes, both police forces will be patrolling. As well as naval forces. I added some Nomad encounters, too.

OK, I'm almost done with the system. Just got one or two more bases to go, and the tradelane traffic, and I'm done with layout. But can someone tell me how to do patrols?!

Patrols can be a bit of a pain. Are you using Freelancer Explorer? Hopefully you are as it makes everything so much easier.

Just add the patrol points as you would normally, but remember that in order for patrol to start at a base there needs to be a person from that faction in the mbase for that base. This seems more picky with trade.

Its best to just use attack patrols for most of the patrols and keep the chances down to a very low 0.05 type amount. Try not to try too much, there are options to add "attack this base" and things like that but if they are hostile, then they will anyway.

If you add these and have trouble with crashes, then decode the systems ini and check that the patrol labels are all unique. Some of the older versions of FLE had a problem with the labels, but i believe that they are all fixed now.

Ah. Thanks, I'll try that. But my main problem was that I couldn't make the patrol end. It seemed like the program wouldn't let me out of "patrol-making" mode. And yes, I use FLE.

You should be able to double click at the endpoint of the patrol. It needs to start at either a base or a jump object, but other than that it should be ok.