I wear 1/2 (short) orthotics and have removed the liner of the shoes so one half of the shoe has orthotic and the other has a hard surface. is it ok? is it bad for knees, etc? should i use toe pads?

Who prescribed them: If you bought the half orthotics over the counter, you need to know why you bought them for. If you have flat feet most often half orthotics they should be fine and should not apply too much pressure to your fore foot. If you have pain in your fore foot then full length orthotics to off load the met head would serve you better . See a podiatrist to help you out with the correct orthotics.

If the orthotic: Is a half device i would place it over the shoe liner or insole cut the shoe liner and place it back in the shoe......You only have to remove the liner if otherwise the device won't fit. But, the toes should have cushion to. Your other option would be to just go full length on the orthotic.

Should be : Fine as long as it is linear.