All of the above limits are MAXIMUMS.
1 S-Rank = 3 A-Rank
1 A-Rank = 2 B-Rank
1 B-Rank = 2 C-Rank
1 C-Rank = 2 D-Rank
1 D-Rank = 3 E-Rank
You cannot spend, say as a novice Genin, 5 C-Ranks, and the use 10 D-Ranks. You can use 5 C-Ranks, 10 D-Ranks, or a combination of the two, such as 2 C-Rank and 6 D-Rank. These will not increase through training, as there are multiple ranks above to eliminate that need.
If abuse of the system is found, appropriate measures will be taken.