Dear Fukuaki
The data are in vivo I supposed? I would first strongly encourage you to activate the remove_median in the filtering section (Common Average Reference, that will get rid of movement artefacts). Then, sadly, there is not really anything you can do, except give it a try and see the results. SC has some built-in mechanisms that should make it, to some extent, robust to small drifts. For very large ones, however, only manual curation and post-processing analysis will help you to resolve them. Here again, some parameters in the [merging] section can be optimized, but this merging step will need the raw results to work with, so first, launch the software :-)
Best
Pierre