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If you are processing your FASTQ files using Cell Ranger, be sure to specify a different feature_type for your Cell Hashing antibodies than any other antibodies in the Feature Reference CSV File. 

If you want to specify each Sample of origin sample IDs instead of using the hashtag feature IDIDs as the sample IDs, you will need to prepare a Sample ID .csv file with the hashtag feature ID IDs in the first column and the corresponding sample ID IDs in the second column (Figure 1).

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It is also possible to use the Merge matrices task to combine your data types and attributes. 

References

1. Stoeckius, M., Zheng, S., Houck-Loomis, B., Hao, S., Yeung, B.Z., Mauck, W.M., Smibert, P. and Satija, R., 2018. Cell Hashing with barcoded antibodies enables multiplexing and doublet detection for single cell genomics. Genome biology, 19(1), p.224.