I think the most general answer here is often: if ingredients might be "overpowered" (or "absorbed"), add them toward the end of cooking.
Slow cookers are great for making flavors homogeneous -- over long periods, all the flavors flow together, with some less flavorful ingredients absorbing flavor from others. In many cases, this is perceived to be beneficial: onions absorb flavor from beef liquid, and the beef gets some onion flavor in return. Or, for example in the case of things like beans, they end up absorbing a lot of the flavors around them and can turn from relatively mild-flavored (or even bland) to highly flavorful.
If you do NOT want that to happen in a slow cooker, the only real remedy is to allow less time for the flavors to mingle. In practice, this may mean adding some ingredients for only the last hour or the final 30 minutes or even 5 minutes of cooking.
With that said: Lifting the lid at that point does have the potential to alter temperature significantly in the slow cooker and to alter cooking times (not to mention the temperature fluctuation introduced by putting a bunch of room temperature or cold food in). So unless you have a recipe that is specifically designed to add in food at a later stage like that, you may also consider pre-heating or even pre-cooking the other food separately, and merely mixing them together at serving time or slightly before. Yes, it's extra work (and for some people defeats the purpose of "throwing it all together" in your slow cooker), but it will help keep flavors more distinct.
It's the equivalent of adding a garnish of fresh-grated cheese or a spritz of citrus juice or a fresh-chopped herb or vegetable on top of a dish before serving -- you do it then, because you'd lose the distinctive "fresh" flavors if you cooked them into the dish for a longer period.