After the brakes have not been used for a while, and you press VERY SLOWLY
on the pedal, does it go to the floor? If so, you've got a leaking master
cylinder (the "well" is on top of that). A leaking master cylinder will NOT
cause the fluid to go down.

If the pedal never actually goes to the floor but still feels soft, you've
got some air in the lines and need a flush.

Aftermarket pads can cause a soft-feeling pedal if they are too hard for
your car.