its not a problem about leaving them underwater, jus make sure you keep it clean so you dont scratch the glass, or transfer parasites from tank to tank
i only get algae in a small spot in the middle of the front and along the bottom. the velcro pad thats on the MF get algae like trying to sweel the flood with a rake. i stuck the media pad to it so its like wiping the algae off. works alot better. i have large one rated for 300g on my 150 and the MD rated for 125 on the 55.