Let's say I have a mid wing and assume the tip to tip span is 100in. But since it is a mid-wing a part of the wing will be inside the fuselage *(assume 10in is inside fuselage)* and not be contributing to the lift. So, for all my calculations should I consider the Tip to Tip wingspan *(100in)* or the effective wingspan *(90in)*?

I know what you are saying but the wingspan is a measurement from wingt\ tip to wing tip, (Consider it as a storage measurement.

When calculating the wing area you are correct in that it is the wing area not covered that is required. Normally just calculate the area of one wing and multiply by 2 or do a full planform area calculation and then subtract the area covered by fuselage or similar.

Regardless the wing span and wing area whilst closely related are not always in linear proportion.

A biplane wingspan is determined by the largest span wing but actually there are 2 wings each of different span and often even different cord.

You must treat the wing area calculations separately to suit the plane you are measuring or designing.

Have fun!