Ive been trying to learn theory for a while and I find it extremely frustrating. I thought it would be best if I go ahead and memorize all the notes for each fret. I downloaded the absolute fretbroard trainer and I can drill it a million times but it dosent help me remember. Does anyone have any suggestions of how you learned the notes.
Learn what a chromatic scale is if you don't already.
Then, learn the first five frets on the E string. Once you have those down, learn the first five frets on the A string. Do this for all strings, while reviewing all the way so you don't forget. Then learn frets 5-10 on all 6 strings. Remember, don't just learn the frets you are working on at the moment, continuously go back and review the ones you already know.

Hope this helps.
Do NOT look behind you.
Try learning patterns too. Learn where the octaves are in relation to each other.
For Example

Once you know where one is you can find the rest.
And try to reverse the testing process and use your own guitar.

Put all the names of notes in a hat and pull one out. Then try to find it in every place on your guitar as you can. As opposed to seeing a note on a computer screen fretboard and trying to name it. Time how many you can do in five minutes. Do it everyday for a week then time yourself again and mark your improvements.

Every once in a while when you're playing a stop and ask yourself "What notes are in this lick/riff/chord?" and single them out and say them out loud to yourself.

When you practice your scales don't just play them chromatically play them in groups sometimes and play them in intervals sometimes so you learn how to put them together in different ways. Always tell yourself the names of the notes as you practice scales.

You won't always be thinking note names when you're playing but if you try to do it as much as possible when practicing scales then it will start to become automatic.

Practice ear training so you can associate the sounds of notes with the note names themselves.