Great question, this is an area where many folks get into trouble right at the get-go. There are several things you need to know when you are setting up your chassis.
1. Tire/wheel package radius
2. Type of suspension
3. How much rake you want on the finished car at ride height.
When you have this info, you can begin your calculations.
The figure for tire/wheel radius is your axle centerline. What you need to do from there is figure out for the front end with your axle how high the frame needs to be over it to give you enough suspension travel. 3" is a good figure. That is your front frame height at the axle centerline. For the rear, the same thing goes. Your rear axle centerline is your rear tire/wheel package radius. Once you have that figure, mock up your frame at the desired rake and see how much clearance you have over the rear axle. If less than about 3" you will have to "C notch" or "Z" the frame to gain the clearance you need. If when you get to this point and the whole car is too high, you will have to modify your frame at the front to get to the height you want, and then reset the rake and determine what you will have to do at the rear for clearance.
Once the frame height is determined it gives you the basis for installing the various linkages for your suspension so when the car is completed the suspension will work as designed. When the car is complete, you then tune your springs to get the car to your pre-established height.
Take your time with this process, it pays huge dividends in the long run!