If that is a Hyper-V server as you indicate, I would not use any of the keys for the host but install Hyper-V server there (which is free anyway).
But if you do want to do it like that - yes. With a limited number of standard licenses you basically must install keys in every guest and make sure you follow the rules as said in the licenses. In case of 2012 R2 standard that is - IMHO and as you point out - using them in max. 2 VM's.
THere are all kinds of other ways to handle licensing, but they all are only applicable for larger installations:
- Use a KMS (Key Management Server), requiting a VL key.
- Use AD licensing (putting the key into active directory), requiring a shared domain forest and... a VL key.
- Using AVMA (automatic licensing virtual machines form the host), requiriing DataCenter licensing.
With a small number of standard licenses you are limited to (manually) registering the license key in the guest, no other mechanism is available.