There is no right or wrong answer to this as you are only building a small system with limited users. From a true modelling point of view then Scenario 2 is correct, but as you say that then makes your solution more complicated for a novice to use.

Scenario 1 will work and be simple to manage (apart from all the blank fields)

So it is really up to you which you would be happiest with.

Personally I would go with Scenario 2 - you will soon get the hang of how to piece it all together for your queries