Deck Stain and Water Putty

This is my first post here. We bought our first home 5 years ago and are finally branching out into fixing up our fixer upper. :) We have an HOA with strict guidelines on stain colors/products, and I submitted an application to use Behr's Antique Oak color. I got a transparent wood stain. After attempting to clean the deck with oxygen bleach (it was too far gone for that level of work) we had it power washed and then took an orbital sander to smooth out the fuzzies and splinters (60 grit for the floor, 80 grit for handrails). The guy at Home Depot, when I was asking about the best application method for stain, told me to get Water Putty to fill in the cracks and knotholes.. We did that this morning, and went to apply the stain and.. it looks awful. :( You can see the water putty right through the stain because it is transparent, and I'm so upset that the "professional" didn't think to ask what kind of stain I was using before recommending that product.

Have any of you used Water Putty before? If I go purchase a solid stain will it cover the puttied spots or will it discolor? Should I go for the deck paint instead? Can I get the color from Behr color-matched for one of the better products like Super Deck?

Deck Stain and Water Putty