I have a red dot mounted on the rail no riser,when I'm on target at 25 yards I am 3" low at 10 yards

That is really strange without a riser.

I am surprised you are that low at 10 yards unless that red dot is high above the bore axis.  I have a safe full of 9mm carbines of different varieties. I zero at 25 yards as with the 115 / 124 gr. bullets I use this gives me the least POI deviation for ranges from "up close" to "far away" (that is "in your face" and out to 100 yards, the working range of a 9mm carbine).

With a 25 yard zero the bullet is "rising" out to the target so anything closer than 25 yards you POI would be blow your point of aim. (bullet hits "low"). It should not hit lower than the distance from the line of sight of the red dot and the center line of the barrel and this is where that 3" low impact becomes confusing if your red dot is mounted low.

As for what range to zero, people will give you man answers. Some just zero for whatever range they think they will shoot the most. Some put on scopes with dials so they can crank the sight into whatever range they are shooting. But then there are those of us who actually can visualize the path of the bullet and adjust our aim point to compensate. For a real marksman this is the way its done. They know how to "lead" due to the speed of their target, the wind, etc. and they know how to "hold over" or "hold under" based on the range to the target.

It is on my new extar pistol,the way the upper is designed it is like a built in riser this is what I assumed made it shoot low up close

What's your height over bore? It sounds like a lot, 5+ inches?

25 yards is my std. zero for all my pistol caliber carbines & pistols. Most of them run optics mounted high.
Some are sighted in for 50 yards like my TNW 10mm carbine and my Beretta Storm 9mm carbine.
If this is primarily for home defense, I'd zero for 7 to 10 yards.