You can't filter imported cost data by custom campaigns, but it is possible to use Google Analytics filters on the imported UTM-tags values.
For example: filter by specific values in the utm_campaign parameter to exclude particular costs.
It is caused by limitations of advertising services on the number of API calls for each campaign. And when OWOX BI requests costs data from advertising service it collects data from all campaigns. So creating more than one pipeline for one account can cause hitting the limit and all such imports will fail.
Therefore, a more correct solution is to divide the campaigns for different sites across different accounts.