T.R.D,
It's not a good idea to use E-manage on 5AT, the original ECU will re-tune/kick back to original form after using the E-manage for a few days, or maybe weeks or months. You will need to re-tune the E-manage all over again, few times maybe. However, not sure about E-manage Ultimate, maybe the original ECU won't "kacau" it. Maybe u can check with your tuner, or go to Trial Tuning and ask.
Other alternatives,
Dynojet Power Commander, Apexi AFC Neo, HKS F-CON IS, etc, or better still, standalone ECUs, such as Apexi Power FC if u can find one for 5AT or HKS F-CON V PRO (for heavy mods) if u have the budget for it.