Aim for E. coli Spike-in DNA (EpiCypher 18-1401) to comprise ~1% (0.2-5%) of total sequencing reads. In the protocol, 0.5 ng is recommended for 500,000 cells. Generally, this can be decreased linearly with decreasing cell number (e.g. 0.1 ng per 100,000 cells). The amount may need to be adjusted to achieve read counts in the optimal range due to variables such as target abundance, antibody efficiency, etc.
For more on E. coli optimization, see this article, and for more on normalizing to E. coli reads, see this article.