Yes, the way both types of accounts trade are different.
The hedging account allows opening different positions in both directions for a symbol. It works similar to MT4. However we still have problems with the hedging accounts because MT5 doesn't add, reduce or reverse the positions as it does in the normal accounts. This are breaking changes by MetaQuots that literally break our experts.
We are working on making FSB Pro compatible with the hedging accounts, but the current version doesn't support them.
It is better to use an ordinary MT5 account if your strategy heavily uses adding and reducing. If you prefer trading several strategies on one symbol, the correct choice is MT4.