Filtered Stats and Incremental Stats on Partitioned table
Incremental stats and filtered stats serve completely different purposes. Incremental stats are not used by the query optimizer. They are a feature designed to make maintenance easier for large tables. They can only indirectly help with query performance because they can make it more practical to keep statistics up to date on large tables.

Filtered statistics are used by the query optimizer (if you write your queries carefully enough). They technically add to database maintenance but can significantly improve query performance in some scenarios.

In summary, you should not have to worry about filtered stats and incremental stats confusing the query optimizer. If you need specific help adding filtered stats to a table please post the table DDL and explain what you're trying to do along with what you've already tried.