Raising the roof of your port is easy. The trick is just to not grind out too much. I could be a little better helping you if I knew what engine you are working on.
The most beneficial thing is blending the bowl area under the valve, and making it flow out as well as in.
When you look inside your valve bowl, you will notice that the short side radius will often form a "shelf". Recontouring that into a smooth curved radius, and depending on the head design, cleaning out what would be obstructions, like the valve guide part that sticks down into the port, stuff like that are more critical than raising the port roof. Its the bowl area where you get the most gains. If you are working on a Small block Ford Winsor or Cleveland, I have a lot more time working on them, I can give you better direction on what to do. However, there are certain givens in all porting jobs, what you should and should not do. Its more important to obtain a good smooth flow passage than to make it bigger.
Rule 1. You dont want to increase the angle of the bend going from the valve seat to the head port on either the intake or exhaust. The idea is to do what can be done to straighten out the curve.
Rule 2. ( You dont want to polish the intake ports mirror smooth. Give them a florentine finish, as a fine polished intake port tends to allow the fuel/ air mixture become unsuspended, allowing the fuel to reconstitute as a fluid.
Rule 3. You cant get the intake side shiny enough. Since you are pushing burnt fuel air mixture out the exhaust, theres no need to keep anything suspended, so the slicker the surface the better. Polishing the exhaust port also aids in preventing deposit buildups as its difficult for them to attatch to a smooth surface.
The only method of porting out an engine is with a die grinder and rotory files, grinding stones, and fine emery cloth darts and wheels.
There is the alternative method that is used with a machine that pushes a mud like stuff through the port to do the job, but that is extremely expensive.
There is also CNC machining and that can get pricy as well.
You have to be ware of raising the roof on the port as there is usually a water passage somewhere nearby and if you get into that, you have ruined the head.
If you want to send me a PM, I will take the time to describe the types of stones, rotory files, sanding points and wheels that I use. With the stones that I use, I can get very close to a CNC machine job.