These are big questions – I hope this covers what you want to know! 
A custom track is an genomic feature track that you create yourself. That can be the original bam or bigwig files, or any that you create by exploring intersections of your data with other annotation tracks.
See the Deeptools tool group since I think it is what you are looking for. More → https://deeptools.readthedocs.io/
To pull in annotation tracks from UCSC, this tutorial is doing something else but has a good example of how to query the UCSC Table Browser – you could adopt this for other tracks they host. → Hands-on: From peaks to genes / From peaks to genes / Introduction to Galaxy Analyses. For other annotation sources, use the Upload tool.
Data can be visualized at IGV, IVG, and UCSC. The fasta index, aka “database” assigned to your dataset is the link. If you click on the visualize icon in your dataset, the applications you can send your data to will be listed.
This topic has a screenshot → UCSC link using Galaxy to see RNA seq peaks - #2 by jennaj
UCSC hosts some model organisms, and those will have annotation from other sources, too. See the Help at UCSC for more. → https://genome.ucsc.edu/FAQ/
IGV needs to be installed but will allow you to create a new genomic backbone even if they do not have the pre-computed.