I do a split boil. Here is how it works... I mash in a cooler and collect my wort in my plastic bucket fermenter. That has about a 6.7 gal capacity. I collect about 6.5 gal to split between my pots. One holds 3.25 and the other 4.25. I put them on the stove at the same time, but the smaller one ALWAYS comes to a boil first. Start timing your hour boil for pot 1. Split your additions as closely as you can to match the volume in each pot. Make hops additions to pot 1. Pot 2 (the larger pot) usually comes to a boil 10-15 minutes after the first pot. This difference in my volume and thusly in the timing has worked beautifully for chilling since it takes around 15 minutes to chill each pot down to pitching range. Just make sure you have the counters cleaned off well. Once pot 1 is cool, I switch the chiller over to #2 and then auto-siphon/pour pot 1 into my fermenter. I wait to take my final OG until I have both batches in the fermenter then pitch. Just remember to sanitize your fermenter while the wort is boiling if you use the fermenter to collect your wort. You will lose a little bit more volume with a split boil so, either top up (if the gravity will allow) or try to account for that and collect a little extra wort. in the .25 gal-.5 gal range.
If you only have 1 pot, then I would mash, collect the wort in a bucket, then boil 1/2 chill, & repeat. I would try to keep the wort covered when not boiling, but then again your boil will take care of any nasties that might want to hang out in nice fresh sweet wort.
Good luck
