Gotta get the rust off first, but once that part is done and you can see metal if you're careful you can blend the paint really well.
You need to remove all of the wax in the area first, and clay bar the area all around where you're touching up. The last thing you want is a little piece of dirt making scratches everywhere when you hit it with the high speed buffer, it will end up looking worse than when you started so make sure its clean. Touch up the areas with paint, try to make it lower than the factory paint level. Let it dry, then cover it again with touch up clear coat - at this point you want the clear to be about level with the rest of your paint, a little higher is OK. Lower is not. Let it dry like this for a full day, in the sun if you can.
Next day, take 1,500 grit sand paper, wet the paper and the area, and sand VERY lightly over the area you touched up. What you want to do is taper/feather it out, so your touched up area is exactly the same height as the paint around it. Repeat with 2,000 grit, then if you really want do it again with 3,000 (will have to buy it from an autobody supply shop, the regular parts stores dont have over 2k - if you know a local body shop they'll probably let you have a sheet). Once everything is smooth, its time to bring back the shine. I use Menzerna Final Polish II - this isn't a compound or wax, it actually polishes the paint and brings a shine to the clear coat which is now dull from sanding. You will need a high speed buffer for this. Once done, it should look pretty close to factory - if you can still see any marks, use a rubbing compound on top of it but at this point you should be able to follow up with a wax & buff and be done.
You may still see it upon careful inspection, but it should be just about invisible. But by doing the clear on top you'll get the closest match to the paint that was already there and wet sanding the touched-up spot and a feathering around it evens it out.