While it's difficult to know what all the drug and supplement interactions are, and to how to prevent any negative ones, recognizing the most important ones can help you to get the most out of your treatments.
First, antibiotics should not be taken at the same time as vitamin or other nutritional supplements. Allow at least two hours between the dosing of these.
Also, if your GI tract is sensitive to antibiotics, consider taking them at separate intervals. While it can be annoying to have to take medication multiple times during the day, it may save your GI tract over the long haul. Having recently started antibiotics, for the first time in nearly five years, I forgot how these things can tear up the gut. I quickly learned that my stomach wouldn't tolerate more than one at a time, so now I space them out throughout the day. Because they all have to be taken with food, this means I'm constantly nibbling, but hey, if it means being able to do the drugs, I can't complain.
If your tummy and guts are sensitive to antibiotics, try taking some licorice chews, slippery elm, peppermint capsules or ginger tea in between doses. A quality probiotic is likewise vital for replenishing healthy flora in the gut that gets torched by the antibiotics. Good probiotics aren't cheap, and the majority that are on the market are garbage, so make sure that you use one that comes recommended by those "in the know" about these things. I took my biotensor testing device to the vitamin store and tested myself for a variety of probiotics. Only one, Udo's, tested well for me. Udo's aren't cheap, but so far, I'm doing well with them.
When it comes to herbs, some are better taken with food, but I have found most to be more potent when taken on an empty stomach. Also, herbs can interact with one another and with medications, so depending upon the herb, you may want to take these apart from your other supplements and medications. Some of the Nutramedix herbs shouldn't be taken together. I discovered this recently when my Nutramedix order for cumanda and noni came with a chart detailing which Nutramedix herbs can and can't be taken together. So every time I get up from my work desk for a glass of water, I make it a habit to take a supplement, so that by the time I've had my eight daily glasses of water (or whatever it is), I've also met my supplement quota for the day, while avoiding any potentially negative interactions. Yes, it's a nuisance, but at least I work from home and am able to do this. If you run around a lot, there may be days when you have to combine stuff, no two ways about it. Don't sweat it. We can't do this dosing thing perfectly.
Homeopathic remedies are best taken on an empty stomach, at least twenty minutes prior to a meal or taking other remedies.
A few vitamins and nutrients interact in a manner which reduces their effectiveness, but most function better when combined. For instance, Vitamin C aids in iron uptake, but reduces the effectiveness of chlorella. B-vitamins and Vitamin A also increase the effectiveness of iron and other nutrients.
For a complete list of which medications reduce the effectiveness of, and/or interact with vitamins, check out: http://harristeeter.com.