I am creating a child stack for a project that lives in a separate directory in the git repo and pulumi is not finding the parent stack because of this. Do I need to organize child stacks in the same directory? I think the answer is yes but just making sure.

I'm not really sure what you mean by "child stack". Pulumi can have references to other stacks (using StackReference), but the stacks themselves don't need to be located together

my main idea is that I have a stack of helm charts I want into install into my eks stack. at present the helm chart stack wants to delete the eks cluster before proceeding.