

Prism can only fit data from one table at a time, and all the data sets must be fit by a single equation you select or create. But you can create this equation in such a way that different data sets are fit to mathematically distinct equations.
When entering a user defined equation, you use multiple lines to define intermediate variables. Each line can have a prefix that specifies which data sets that line will be used for:
Prefix 
This line applies to 
<C> 
Data set C only 
<~B> 
All data sets, except B. 
<A:D> 
Data sets AD. 
<~A:D> 
All data sets except AD. 
<A:J,3> 
Data sets A,D,G, and J (every third data set between A and J.) 
<~A:J,3> 
All data sets except A,D,G, and J. 
Here is an example. It fits column A to a model that defines total binding and column B to a model that defines nonspecific binding only. The first two lines of the equation are evaluated for all data sets, the third line is only evaluated for data set A, while the last line is only evaluated for data set B. To fit this model, you would want to set the constraint that the parameter NS is shared between data sets.
Specific=X*Bmax/(X+Kd)
Nonspecific=NS*X
<A>Y=Specific + Nonspecific
<B>Y=Nonspecific
<A>Y=1/(1+Ka*X^h)
<C>Y=(Ka*X^h)/(1+Ka*X^h)
The equation above seems clear at first. The first line is for data set A, and the second line is one for data set C. But what if you asked Prism to only analyze data sets A and C, skipping B? Now it is a bit ambiguous. Does <C> mean data set C, or does it mean the third data set included in the analysis? Prism uses the second definition. So you need to enter the equation like this.
<A>Y=1/(1+Ka*X^h)
<B>Y=(Ka*X^h)/(1+Ka*X^h)
Now the second line is for the second data set, which in this example is data set C (since only A and C were selected in the Analyze dialog).