Personally I'd scrap the stock pads altogether and pick up a set of supercartrages for your 350. These increase the bio capacity of the filter and use washable...very inexpencive filter pads for mechanical filtration. We have several dozen of them running on our emporers and wouldnt use anything else.
To directly answer your question however... No washing the pads in the sink wont hurt anything as long as you leave the bio wheels alone. The stock pads and even some of the aftermarket pads that are sold for the marineland filters start to break down after 3 or 4 cleanings or so.
You used to be able to buy plastic media frames for the penguins to replace the stock pads. these are not available for the emporers but I still have a few running on various tanks and they work well.
Note: not all of the pictures I posted are for the marineland filters but thats all I have on this computer at the moment and they should give you a good idea of what I'm talking about.
You can pick them up on line for a lot less. Several vendors on Ebay carry them along with a lot of the better on-line shops. You can cut replacement pads as necessary from any commonly available pad sheets.
One other advantage is that I keep spares and can clean all the filters on 15 tanks in about 10 minutes....
i also have been using media baskets .. .. how often do you recommend changing them .. and can you clean those under tap ? ..... and one more question ... a friend suggested i could bag carbon and put it in the media basket space closest to the tank (for holding purposes) and it may help even more as far as filtration ... what do you guys think?
I don't care for the regular use of carbon or zeolite for that mater. IMO if you have your set up correct it's not needed and represents an unnecessary expence.
Thanks for the links DM but I prefur the supercartrages. In fact they can even turn second hand wispers into very good filters. I have a box full of them for emergancy use from various tank deals.