Hi Jasmine!
As for the pills, I'm not sure if there really is any benefit to dividing them up vs. taking them all at once. I usually take my hormones in the morning, it's just easier for me so I don't have to worry about it during the day.
As for the other health issues, just note anything out of the ordinary and let your endo know. Symptoms vary, so if you notice something different or feel something may be wrong, be safe and let your doctors know. I have been on hormones since early 2007 and only once had leg cramping, but it turned out to be nothing serious. Regular blood work per your endo and good communication with your doctors is the best way to pursue healthy hormone replacement.