With that size pot, you will have to top off with a few gallons of water in the carboy (i used spring water when i did this). This of course means that since you will be diluting your wort after the boil, you need to be able to mash enough grains to reach the gravities you are shooting for.
So for example, if you are planning on brewing a simple pale ale and you want your OG to be 1.050 with a 3 gallon boil and five gallon batch here is how it will work. (Let's assume 60% efficiency since this is your first batch)
You will need to mash approx 11.5 lbs of grain. You can do that in a 5 gallon MLT cooler, but a ten gallon would be better so that you could also brew much larger beers.
So you then collect 3 gallons of wort with a 1.084 preboil gravity. Boil for 60 minutes and then add approx 2.5 gallons of spring water to the carboy.
That is all very doable for your setup, and then once you have done a few brews that way you can upgrade your pot to a larger one. I currently do all grain in my kitchen. I use 10 and 5 gallon cooler mlt's (depending on how much grain I am using), I have a 8 gallon pot for the boils, and I can bring 6.5 gallons of wort to a boil in about 20 minutes.
When I had a 5 gallon pot and was doing partial boils, I also did partial mashes where I would mash up to 12lbs of grain, and then during the last 15 minutes of the boil, add up to 2 lbs of extra light DME to hit my target gravity. I made great beers like that, light years better than my all extract attempts.