So I have seen that its not good to do to much with a puppy. Xena is 3 months old and I dont want to overdue the amount of exercise we give her but she seems to love it. I usually walk her for about an hour in the morning when I get up before work. Usually go about a mile or so. My wife and I both come home during the day and let her out for about 15-20 min each but she doesn't really get a lot of exercise then, its more of a bathroom break for her. Then we usually walk her or take her to a dog park or something in the evenings. She still tends to have a lot of energy when we are at home and plays with me in the apartment and stuff. Is this a safe amount for her to be doing at this age? She seems to like it, but I don't want to cause problems later because she was doing to much to young.

The rule of thumb is 5 minutes of walking per month of age, at a time. So at this point 15 minutes walks would be best. You can still walk her a few times a day. Training is also a great mental stimulus that can tucker them out.

From everything I have heard, it sounds like you are doing ok. As long as you aren't trying to run hard with your puppy and force her to go longer than she feels comfortable, then she should be ok. When I took my pup to "kindergarten" last summer, she was about 4 months old. We did some basic agility, nothing too major. But the trainer did tell me that we didn't want to get into any heavier agility training until she was at least 9 months old because the running and jumping can be tough on their joints while they are still growing.
So it seems like the key is to just let your pup let you know how much she needs. As long as you are watching her and notice when she's starting to get tired, and don't do any heavy running. Especially in the summer heat, give her plenty of water too. When she gets closer to 6 months old, you will be able to increase the amount of exercise, especially as you notice that her energy level is increasing. Exercise will be even more important between about 6 months to a year, because that will give her an outlet for the sudden burst of energy, or as I've heard them called "the puppy zooms"!
If you take her on shorter walks, you can have a short training session afterwards like Keyda81 suggests. The training sessions are great after you get a little of that excess energy out. She should be a little more focused then for you too.

I used to go on mile walks when Maggie was really little. I got alot of toys to play in the evening. I actually stated hiking with her at 8 months.