Do you want to drain 1/3? If you do, I guess that's fine.

But, simply knowing that your CYA is greater than 100 is not a good starting place. If it's 400 ppm currently, and you drain and replace 1/3, it will go down to about 265. If you do the same thing 2 more times, it will go down to about 120, and STILL be over 100, even though you will have added enough water to have done a 100% drain and refill.

How are you testing? If it's with 'guess-strips' -- or a 'guess-strip' reader, you really don't know anything at all. The CYA test is the worst of a bad bunch of tests, on strips, and can be horrendously inaccurate. Probably your FIRST step, if you are primarily concerned with your CYA levels, is to get a reasonably reliable result from a GOOD test kit, using a distilled water dilution.

Get one of THESE kits:
HTH 6-Way Test Kit @ Walmart
Taylor K2006A (3/4 oz bottles) @ Amazon
Taylor K2006C (2 oz bottles) @ Amazon
AND a gallon of distilled water from Walmart (or whatever big box store you like).

Then, collect mix 1 cup of POOL water with 2 cups of DISTILLED water. After stirring, do the CYA test, and multiply the result by 3. The CYA test in these kits is not great either (much better than strips, but still not great!), so looking at the videos here, http://www.poolforum.com/pf2/showthread.php?17157 , may help. The HTH 6-way drops is ALSO a Taylor kit, so the videos still apply somewhat.