Hi Chris,
There's no problem with that. Lots of people pull back the cover to add algecide or chlorine.
Do you have a submersible pump? I have one with a long output hose and I used it this season to circulate chemicals. The hose moves around the pool and works quite well.
The chemicals might work their way around the pool naturally but I'd feel better if I could circulate them somehow.
Lenny

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) and put some Polyquat algaecide in, then reclosed the corners, then I added some more in the skimmer openings. With only 2 anchors open at a time, there's no risk of anything harmful happening. Lenny's idea of using a submersible pump to move the water around is a good one - I may have to try to do that sometime.
) However, the water temps are a little more comfortable every day and I think you are doing the best thing for your pool by adding chems and circulating the water now - at this time of the year, a minimal dose of cl and a few hours of pump run time will save you many headaches - as opposed to waiting until the water was temperate enough to swim, and then trying to get it ready for a weekend swim party 
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