You could take the calcium w/ meals and the levoxyl at bedtime.
It may be a few weeks before the remaining parathyroid "wakes up" -- hopefully it will "wake up" if not then it's long term calcitriol and calcium - usually the calcitriol is once a day and calcium 2x/day if it's long term.
Speaking from experience as a patient in a similar situation (TT in July '06), it will depend on your calcium levels. You'll have blood tests to check your calcium until your levels stabilize. They will probably also check your PTH (parathyroid hormone) levels to see how your remaining parathyroids are working. Most people can go off the calcitriol and extra calcium after a few weeks. Some--like me--will be on these meds indefinitely. I recently went off the calcitriol after 18 months; so far so good. If you end up on calcitriol long term, please post again over on the thyroid support forum. There are others with related stories who have good advice and suggestions.
I take my Levoxyl at 6 a.m., and my calcium at 10:30 a.m., 3:30 p.m., and after dinner.