understand it in this way:
the free amino acid pool itself appears to be structured
= The localization of free amino acid in the body appears to be regulated in certain way.
in the sense that = because ( considering the following example):
1.the extent to which amino acids are concentrated inside muscle cells varies with the type of amino acids
= different amino acids have different concentration in muscle cells
2.the distribution ratio of different amino acids across muscle membranes alters during different circumstances
= the distribution ratio of different amino acids across muscle membranes also changes under different circumstances.