I'm using an AR, so maybe the starting delay between me pressing start on the AR and the game loading up is throwing a wrench in it. Should I try to compensate for that and if so how would I? (using Eontimer)
Using an AR with Eontimer is do-able, as I am proof, but it can cause errors, delay errors.
I don't know if the delay in BW are just odd or even or a mix but if you use a AR, you will hit a mix of delays.
But to your question, yes you will have to compensate SR by pressing A at a certain time.
What I mean
As you know, you cannot SR an AR and still have the code function, so you cannot SR, instead you will have to experiment with pressing A to exit the AR and load the game at a certain time to compensate for SR.
My advice, you should press A ~1.5(absolute minimum)-2.5
I usually "press start the game with code" around 2.0 and I am usually -+5 of delay, but usually +-1.
You will need to be patient doing this
Edit:
To add with johto (Who ninja's me X.X) just said, you can exit the AR when the 1st timer hit zero, but I pretty sure you be off by some amount, should be lower.
If you do it the way I do, you should be either a little high or low