Video encoding with NVENC doesn't make use of SLI. It just uses one GPU. That's not a limitation by voukoder, its how NVIDIA designed it.
Furthermore frames need to be rendered first before they can be encoded. This step is done by premiere and can not be accelerated by any voukoder component. You might attach your logfile here.
You'll also find more details here: Voukoder Performance Analysis
(I should really do a youtube video about this)