For all the small holes and ratty areas where may you have a large split or a small knot hole you can use paintable adhesive caulking. Easy as can be. just use a screwdriver or something to pick out of rotted edges so that what is left is solide. squeeze a little caulking compond in there or along the crank. Smooth it with you finger and paint over it when it is dry. (don't do that if staining, the stain won't go into the caulking. You can do lots of touch up work with that. It's a beautiful thing.
Large holes need a different plan of attack depending on what the layout of the deck is. Say, for example, if you had a higher deck and could walk or crawl under it, the best thing to do would be to put some "backing" on the board behind the hole. In other words, use the adhesive caulking compound to "glue" a small piece of wood slight larger than the hole underneath the hole. Then when that has set and hardened. Go back to deck and fill it the hole with wood filler which can't fall out due to the backing. Works well if you can get under the deck, not so well if you can;t. Sometimes the hole occurs in short piece of decking wood and you can pry the decking board up - flip it over and put backing under the hole- then re-nail the board down again and fill the hole. Works okay if you have a small board that is still strong and just dropped a know and left a big hole. Does not work so well if it is a longer board that has aged-out because the board is likely to fall apart even more if you pry up a long section.
Anyway. for the large number of ratty little blemishes and very small knot holes, consider an adhesive caulking compound. About 3 bucks a small squeezable tube. Just apply it by squeezing directly from the tube. then use one nice clean swipe with your finger to smooth it and then let it set. It's a beautiful thing.