(I've edited for Springer, Elsevier, and other families of journals for about 15 years.) A common, consistent, and reasonable convention in academic writing is that "respectively" is used to indicate a one-to-one correspondence between the elements of two or more (equal-length) lists in the same sentence.
The two circles were labeled A and B.
Consider circles 1 and 2. Their corresponding radii are r1 and r2.
Consider circles 1 and 2 with radii r1 and r2, respectively.
The radii of circles 1 and 2 are respectively r1 and r2.
Other conventions exist, but this one is particularly easy to apply because you need only consider a single sentence at a time and because you need not assume anything regarding the reader's knowledge. As above, "respectively" can be placed directly following the verb without commas or at the end of the sentence with a comma:
G and E respectively represent the shear and Young moduli and ri and ro the inner and outer diameters.
G and E are the shear and Young moduli, and ri and ro are the inner and outer diameters, respectively.