Characters like Helena who have the Bokuho duck (BKO), you'll need to learn how to apply the 2P effectively. You'll also want to figure out when it's appropriate to put your 6P or 6K mids on Helena when she wants to go BKO or go for a low.
The thing about fighting Helena as Ayane is that you have to learn how to keep the BKO duck in check because that is the only weapon Helena has that is pesky against Ayane up close. Most of the time it'll come down to 33P (i13 mid and high crush vs jabs), 3P (i12 mid, her fastest mid), 1P (low punch and high crush), 5K (i12 but loses to Ayane's 5K in damage), jab/PP (i11) and attempts to go BKO.
Jab from Ayane beats everything except for 33P, BKO and 1P. 2P loses to 3P, but beats 33P, BKO and 1P. 6P&6K loses to 3P flatout in speed, but 6P can high crush jabs. These things are really going to be determined based on what the Helena player normally favors during the neutral situation.
If she likes putting the mid punches out often, remember that hold on read will beat the mid. But more often than not, the match in CQC usually comes down to Helena fighting the low jab, and Ayane fighting the 3P and 33P. Our low jab forces Helena to worry about it more than anything else because it stops everything she can do except for 3P but that loses to jab/5K/hold/block.
Our options open up a lot more once Helena understands that the 2P will be there to be any sort of momentum she's trying to build to a halt.
As for applying a better range game, I would strongly advise practicing the Integrated Movement and different strikes in training mode. Just set the dummy to Guard All so it blocks and stays still.
Try to mess around and get used to the following;
5K, 3P, 3H+K, 2P, BT2P, BT2K, BT6K, P > BT8P, P4P, 3K
Just mess around with the above at different distances so that you can get an idea/handle on them at range(s). Using follow ups to the strikes that have a follow up is also your choice. There are definitely more options than the above, but I suggest these as a start.
For the Integrated Movement, that bit will take time to master because it's honestly
not easy to grasp at all. But it is definitely worth practicing because I believe it to be crucial to her play (I view it as a strength to this character). Her movement actually allows you to apply pressure at different distances.
I would recommend checking out this thread if you already haven't;
http://www.freestepdodge.com/threads/homework-time-footsies-and-spacing-101.4522/