You have to hold your head properly to avoid that issue. Also, if you are really clogged, you may have to pour more slowly and push a little air through your nose too. In such cases, you may not can avoid having a little trickle down your throat, however, it shouldn't be much. Usually, as stated, that means you're holding your head a little off from proper position. Be careful that you aren't shifting your head position too much when using one hand to hold the pot as opposed to the other.
I think the Neti Pot is great, particularly for nasal allergies, but also just for feeling clean and refreshed.
This is the one I have.