I second the suggestion to contact AOPA.
My understanding is that you have two options;
First, you should try to take an approved alternate test. The test is administered by an opthamologist and if you pass the results are sent to the FAA. The FAA will then send you a letter that basically states you meet the color perception standards and do not have to be tested at future medicals. This is the way to go. You will not have a SODA, so it shouldn't be an issue in hiring.
Second, if you don't pass the alternate test, you make arrangements with the FAA for a SODA. If you opt for the SODA first, I don't believe you can try to take the alternate test. The SODA test for all three classes of medicals is the same. I believe you have two, maybe three chances to pass the test. For me, the FAA Inspector stood outside with me and had the ROC tower shoot the light gun in my direction. I identified red, white and green and the test was over. This was 15 years ago, so it may have changed some.
Good luck.