Pathfinder 1E New to DM

I am planning a campaign and I have everything situated except the battles and dungeons. What is the best way to determine what level the monsters should be so I don't destroy the players but they still have a challenge? How do you determine total Challenge rating for a fight?

Perhaps this is what you need?

http://paizo.com/pathfinderRPG/prd/gamemastering.html

Remember that the above link is a guideline, mostly for experience from an encounter, not necessarily how well the party will do in the encounter. Finding the balance can be difficult. Wading through goblins is fun, but the best gaming stories are those the players feel their characters barely survived. And CR doesn't always cover it.

Things the book says that I take into consideration:
1. Player experience and cleverness. An experienced player can handle higher CR, and an inexperienced player can get pounded by an equal CR.

Creature/NPC Intelligence/Wisdom. If the creatures/NPCs are adults, and they've survived that long in the wild/dungeon/city, they've seen things, faced threats, and survived. They know don't focus all your attention on the big armored guy, they'll run & hide to come back later, or they've seen magic before, and either specifically target or avoid those who have it.
My rule of thumb is, Int/wis of 8-10 is a human level mind, act it. And if the creature has a higher int/wis than some of the players, then it can out-think them and even partially predict their actions. If it's grossly higher, then it'll likely be able to predict the characters choice of actions. Though you can make Int/Wis rolls for that if you like.

Give your players a simple little adventure to test them out before you jump them into the campaign you worked so hard on.

As a basic rule of thumb, I've found that a CR of APL+2 tends to be the sweet spot for non-boss battles.

Also, even a lowly hobgoblin or kobold can a frightening challenge if given a level or two in an NPC or even a PC class.

Usually you'll want a small group of monsters, with a CR equal to the average level of the party +1, for a normal encounter, or +2 for a difficult encounter. That is assuming you are not just throwing one creature at the entire party.

So for a level 1 party of about 4 players, a group of 4 to 5 CR 1/2 zombies is not a very hard encounter. But if it's three zombies, and one CR 3 enemy, that fight might be a lot harder.

Most enemies aren't so tough if they are alone, and the entire party can easily gang up on them. But give them some lower CR minions, and the players will have to divide their offensive power.

The design of the group of enemies is also important. A group of 4 CR 1/2 skeletons with swords is not a big deal. But if two of them happen to have bows, and are standing on higher ground, that makes a big difference. Do the players have ranged weapons to deal with them? Or do they need to first climb a ladder to reach them, while getting hit with arrows all the way?

And not all players are the same. Their strategy and equipment matter a lot, as does that of the enemies. So if you are entirely unsure of the strength of the players, throw a weak encounter at them first, so you know what they can handle.

I have found that a single high CR creatures does not make for a very interesting or challenging encounter. Lots of PFS scenarios end with an encounter like this which ends up being very anti-climactic. The main reason is how the action economy works. Say you have a party of 4 characters at 4th level. The last fight in the scenario is against an 8th level/CR 7* NPC. The NPC is tougher that any individual PC but gets 1 set of actions to their 4 or more sets of actions. The PCs, as a group, act at least 4 times** for every time the NPC acts. The NPC just gets overwhelmed and taken down in short order. There are exceptions where a combination of abilities and terrain make this less likely but this is the usual outcome.

*NPCs are usually not as well equipped as a PC of the same level which reduces their CR.
**More if they have things like animal companions or eidolons.