Guess I may not be fully understanding the question. But if you are doing a 5 gallon batch, you want a 7+ gallon boil kettle. You eventually want to figure out your boil off rate and compensate in the beginning of the boil. I would assume in 60 minutes, you would figure between .5 and 1 gallon of boil off. Factors affecting this are kettle geometry (fatter, shorter kettles boil off more), and the moisture level in the ambient air (cool/dry weather boils off faster).
So you fill your boil kettle to your 6 gallons or so and add half of your extract. Add your 60 minutes hops once it starts boiling, and add the rest of your hops per your schedule. With about 10 minutes to go, add the second half of your extract (this method leads to less carmelizing of your extract, so your color is closer to intended). This is also a good time to add Irish Moss and any yeast nutrients. Then at flameout you want to chill to pitching temps as quickly as possible. Most effective is a wort chiller. The cheaper ones are called immersion chillers, and send cold tap water through a 1/2" x 25' or 50' copper coil immersed into your wort, and out into a drain. You can either pre-sanitize the chiller with Star-San or drop the chiller into the boil for the last 5 minutes or so and then hook up to water once you get to flameout.