You are using the neti pot incorrectly. Filling it with just water will always cause your sinuses to hurt like crazy. Here's what you need to do instead:
Drop about 1/2 teaspoon of plain (not iodized salt) into the pot. Fill the pot about 1/4 with HOT water. Stir the salt in well, then fill up the rest of the way with warm or cold until the pot is full of lukewarm to slightly warm solution. (If you only have iodized salt, use it for now, but get non-iodized salt as soon as you can.)
Now, bend over your sink until your face is more-or-less parallel to the sink, and quite close to the sink.
Tip your head to the right. Holding the spout of the pot snugly in your right nostril, slowly pour the solution into that right nostril. You will find that the salt water runs out of your other nostril. It may make you gag a little. If so, just cough a little, but keep on pouring.
Now, refill the pot, tip your head to the left and do the same thing on that side.
When all the solution is gone, keep your head low in the sink, and firmly blow (that's right, blow right into the sink) through your nose at least three times. This is called bellowing, and is necessary to remove the excess water from your nose/sinuses. You are finished! Your nose will probably run for a little while. Just gently blow your nose with a kleenex as you would usually do.
Now quickly rinse any gunk out of the sink. You can clean it more fully later, but rinse right away with pretty hot water. Snot dries on quite hard if you let it dry at all.
When done correctly, nasal lavage (just means nasal washing) is quite soothing and helps a LOT.
Once you are accustomed to doing this, there is a second step you can add for even deeper cleaning. Do the above rinses, then do the whole thing again, but now you may inhale gently and intermitently WHILE pouring the solution into your nostril. This generally causes even more gagging and coughing, but it works wonderfully at clearing gunk out.
I have suffered from sinus problems (allergies and terrible infections) for more than 20 years now, had the surgeries, taken the drugs, etc. But I honestly think that using a neti pot has helped more than anything else I have ever done.
I hope this helps you. I really do know how terrible sinus pain can get!