If you don't have a filter you will need to do a 50% change and a 100% change every week. You obviously need to take him out for the 100% change (try and scoop him up in the cup rather than netting him if you can). I don't know if you can fit a gravel vacuum in your tank or not. If you can, I think that's the easiest way to do water changes, just use it to siphon out half the water on your 50% day, and then do a nice gravel vacuuming on the 100% day. If you don't want to use this method/can't find a gravel vac to fit your tank, you could just pour out the water...if you use this method you should rinse your gravel when you do your 100% change. You could also scoop out the water with a cup, this is the most time consuming method in my opinion, but if you don't have a gravel vac and your tank isn't in a good location to pour out the water, it's definitely an option. If you scoop out water, make sure you agitate the gravel so all the debris and waste come up out of the gravel and you can scoop it out with your cup.
If you do have a filter, I'd do two 50% changes per week. You don't want to rinse the gravel if it's filtered (first of all, you're not doing 100% water changes so it would be harder to rinse it, secondly beneficial bacteria will hang out in the gravel of a filtered tank) so you will either need to use a gravel vacuum or you'll need to do the scoop method (making sure to stir the gravel to get the nasties out).
People say it's less stressful for the fish to leave them in the tank if you're doing a 50% or less water change (especially because with a small tank you'll need to do multiple water changes per week), but it depends on your fish, your tank size and the method you use. You definitely want to take him out if you're pouring out the old water, and if you're using a gravel vac in a tank that size, I'd play it safe and take him out. There are horror stories about people's fish getting sucked up by the vacuum, and in a tank that size it could be hard to avoid him. If you use the method where you scoop water out with a cup, you could leave your fish in.
You could also use plain airline tubing rather than a full on gravel vacuum to siphon out water (this won't clean gravel so you'll still need to rinse it if you don't have a filter, and if you do have a filter you'll need do the stir and scoop method several times to make sure the gravel is clean), I'm sure you can leave the fish in the tank if you siphon with airline tubing, just be careful to keep the suction away from the fish.
So how you do your water changes really depends on whether or not you have a filter, but either way you have several options to choose what is easiest for you and your fish! In my filtered 2.5 gallon I use a gravel vac to do my two 50% water changes, and I catch my little girl in a cup so she's out of harm's way for the duration of the change. She doesn't seem to mind it so that works well for me, but some fish are stressier than others, so you have to figure out what will work best for your fish.