1. I normally encourage "collateral" branches, since they can always connect your ancestor to somebody else. I do not encourage including groups of individuals that do not connect to your tree. They only serve to consume resources and create false matches.
2. If you have any names with "non-English" characters, you need to specify UTF-8 character encoding, if your genealogy software offers that option.
3. You can upload a GEDCOM with more than 10,000 people, but only the first 10,000 will be used in comparisons. However, all names will be included in searches.
4. You can link any combination of multiple kits, multiple individuals, multiple GEDCOMs.
5. Large GEDCOMs (over about 10-12Megs) sometimes cause problems during upload. File size can be reduced by not including notes and resources when you export. If it is still too big, you can split a GEDCOM into 2 or more smaller branches.
John