How the ace side count is used depends on the main count you're using. Hi-lo counts the 10's as a -1, so the surplus/deficit aces will have the same value of 1. Since the ace is already reckoned in the main count, the aces are compared for playing decisions like insurance. If the running count is +6 and you're 4 decks into the 6d shoe, you should expect to have seen 16 aces, four for each deck. If instead you've only seen 14, that's two surplus aces that have yet to be played. I believe you subtract these surplus aces from your running count, so +6-1-1, to get a RC of +4, so a TC of +2 for this playing decision. Had you not had the side count, your TC for the decision would be +3 because you wouldn't have known to adjust it. Similarly, if you've seen more aces than normal, like 18 instead of 16, you'd add those extra aces to your count for insurance decision purposes.
In ace neutral counts the aces work differently. They're used to get a betting count. The main count is used for insurance and playing decisions. In HiOpt2, the 10's have a -2 tag, so the surplus/deficit aces also have an adjustment of 2. If my RC is +6 and I've only seen 14 aces instead of the 16 like I should have at 4 decks in, I adjust my RC by +2 for each surplus ace to be played +6+2+2 = +10 RC for a TC of +5, so I bet as if the TC is +5. After I get my cards, I play them as if it is +3 TC provided the count hasn't changed because playing decisions are based off of the main count.
Is it worth it? That's up to you. I side count the aces in shoe games. I play both pitch and shoe games. I personally feel I'd make a lot of mistakes if I used different counts for different games so I keep it simple and just use HiOpt2 for everything.