The way in which I would handle a situation like this would be to ask for more clarification in person (only if this is possible, I realize that some people work remotely).
If doing so solely through e-mail, keep in mind that your boss may be very busy at times and may overlook details in emails or just skim through them to get a basic idea. If it is an urgent matter, I would flag the e-mail as important (Please use this sparingly, see also: Overusing high priority flags).
For the content of your e-mail you would likely want to use a list or state your intent (based on what you believe to be more important at the time)
I will handle the issues you sent me in the following manner.
1) Issue 1 (Whichever you think is more important)
-Step to reach goal
-Step 2 to reach goal
2) Issue 2
3) Issue 3
If you have any objections or would like me to redirect my focus elsewhere,
please let me know.
Depending on your relationship with your boss + a combination of how casually your office communicates, you can keep or kill some of the formality. The first sentence could possibly come across as a bit bossy, so if anyone has a suggestion to clean it up it would be appreciated.