I also play with 1:6000 scale. I use pipe cleaners (you can cut them with heavy scissors and they bend as well as being cheap and readily available) for smoke. White for chemical and black for funnel. I use small puff balls for markers. Red for fire, White for non-penetrating hits and black for penetrating hits. I do use Litko markers for radar contacts and I use their smoke markers to outline squalls as they are easy to move every turn. I also use Litko markers for evasive maneuver as I use all the optional gunnery rules. I also use Litko markers for EDR fires in night actions and their illumination markers for star shell. I've decided to standardize the size of my squalls (this is always a work in progress, even after 40 plus years) 3" diameter for small. 6" for medium and 9" for large. I'll cut them out of mat board and use the Litko markers for when two or more squalls merge as happened in PB vs Convoy 2. Now, I don't use cementers for range. I use inches and 1 inch is 500 yards. I do this because in 1:6000, 1 inch equals 500 feet. That makes the math too hard for me and I play with 1 inch = 500 yards or 1:18000 as that makes the math easy. as you can see my way of doing this subject to change when I find something I like better for whatever reason takes my fancy. So, I love to hear how other people do this as I expect to find a better way on occasion. And if I've given you any ideas here that will make the hobby better for you then I'm just ecstatic.
PS I don't use flotsam and jetsam markers as I do not keep track of atrocity points. This is war after all, and IMHO mercy is for the merciful and I do not define someone trying to sink me as merciful.