"Can you use VNAV with altn EEC?"
The selection of ALTN EEC's may stop you using the Autothrottle, in which case, you won't be able to use VNAV to its full potential (This is especially so on those aircraft which use EPR's as the primary engine parameter, such as Rolls Royce. Selecting ALTN EEC's will revert the engines to N1 control instead of EPR control. The A/T cannot set the thrust if the EPR is unknown).
Regards.
Q.