Yes, you can still use the hi/low boost function with the HKS actuator, the 4E-FTE specific kit comes with a hose T piece so you can plumb the solenoid back in.
The T piece goes between the turbo compressor nipple and the HKS actuator, the take off hose connects to the hi/low boost solenoid and the other hose from the boost solenoid is connected back into the air intake between the air filter and turbo inlet (the stock EFI pipe has a nipple for this hose. If you no longer have the stock EFI pipe installed, then you would need to attach some form of mini air filter to the end of this hose). The solenoid needs to be in hi boost mode when you start adjusting the actuator.
Personally though I wouldn't bother plumbing the hi/low boost solenoid back in and just link a hose straight between the HKS actuator and turbo compressor nipple.