Make sure you get the probiotics/acidophilus from a health food store as opposed to a drug store. They are of MUCH higher quality and will make all the difference! If they are to be refrigerated, this will assure you they are of high quality and contain live bacteria. Probiotics with dead bacteria are basically good for nothing.
The antibiotic will not kill the acidophilus. It is always a good idea to take acidophilus while taking antibiotics. Actually, it's always good idea to take them anyway. The acidophilus will help to keep good bacteria in your body since the antibiotics will be killing it off. Trust me, get the best ones you can find. I was recently on a L O N G course of a somewhat hardcore antibiotic and I'm paying for it now. It's going to be a while before my bacteria levels are back to normal. Btw, I've never heard (or read) that they need to be taken at a certain time.
Also, eat a ton of yogurt while you're on the antibiotic routine. This will also help to keep your good bacteria levels up :)
Any time I have taken antibiodics and knew it would result in a yeast infection, I took the yeast infection medication the day after I took the last antibiodic. Mostly because the antibiodic is much more powerful.