You can specify different normalization methods for different molecules.
The default normalization method can be specified at "Settings > Molecule Settings > Quantification".
You can override that setting for individual molecules using the Document Grid.
There is a column called "Normalization Method" that you can show in the Document Grid.
If you would like to learn more about using the Document Grid you should look at the Custom Reports tutorial:
By the way, if you want to use a different, unrelated molecule as the internal standard for a particular molecule, then you should use the "Surrogate Standard" feature. There is a tiny bit of documentation about surrogate standards here: