Nexium is a short term drug only (the package insert states 4 to 8 weeks to treat GERD). There is a very good reason why acid blockers are short term drugs. Low stomach acid reduces absorption of nutrients such as iron, B12, folate, calcium and zinc; affects digestion of protein, carbohydrates and fat; and increases the risk of bacterial overgrowth and fungal infections.
I posted a lot of info on another thread about reflux and treatment options: http://www.medhelp.org/posts/GERD-Acid-Reflux/HELP-for-GERD-sufferers/show/1657073
An example of how you might want to take your supplements: take synthroid on an empty stomach, half an hour to one hour before breakfast; vitamin B12, vitamin D and prenatal vitamins for lunch (vitamin A, D, E and K are fat soluble vitamins so eat a meal containing fat for better absorption); metformin with the evening meal.
You can switch this around but avoid taking vitamins with synthroid (calcium and iron can interfer with thyroxine absorption) and metformin (can inhibit the absorption of vitamin B12).