It's a problem I have and I've seen at least one other user have where they'd look at Soul Reaper II and think, "This is really good I need this!" but then they buy it and think "wow, nothing happened?", or other cases like equipment %ages adding together and daily CpS + random box CpS, but bonus CpS from food multiplies together. Or, apparently you can buy an upgrade that gives you more souls from the bow, but it also gives you more souls in Chest Hunt.
To increase clarity, my suggestion would be to put in some symbols to show a relation. I've attached an example where I've put a little white scythe symbol next to the Soul Reaper modifier, people could see that and think "this might add to an existing multiplier"
or in a Chest Hunt there could be a bow symbol next to the slayer points and people might think "oh this is affected by bow upgrades"
every fine detail