I'm struggling with that right now too...it can be tough. I was dx'd November 2010 and each time I increase my thyroid meds, it takes awhile to adjust. In the meantime I feel jittery, anxious, with a racing heart, and then the hypo symptoms as well. Fortunately after a week or two I start feeling better than ever.
In November I started 50mcg Eltroxin. That was by far the worst period, I had been without adequate thyroid hormone for so long that it was a huge jolt to the system. I missed about 7 days of work. Then in January I went up to 75mcg, and was off work for 5 days. Right now I'm needing an increase and have missed 4 days.
Fortunately, my workplace (specifically, my immediate supervisor) has been very understanding in letting me take the time I need to adjust and feel better. I take sick days, if I run out I'm allowed to take vacation days, and if those are gone I can take unpaid sick days. I am very grateful for this, although I do feel guilty, like I'm playing hooky from school or something. But that's my *thyroid brain guilt*.
You know what the worst part is? Gauging when I can come back. Trying to figure out if I think I can do it, make it through the day, be able to concentrate. Coming back after missing a few days is scary, quite frankly. Fortunately it usually only takes a few days to feel like myself again.
Sorry for the novel. This issue just happens to be near and dear to me right now!