1. I have a song that has no vocals but clapping. I was able to chart the clapping but Magma still wants a vocal note and will not create a CON file without it. What I did was just put a single note at the way end of the song. Is there another workaround for this?
I don't know that the game will actually support a vocal chart with only percussion/clapping notes, but I don't know that it won't either. You can try using Magma's MIDI override option to insert a MIDI without any vocal notes after the build process. But definitely test your custom before uploading it, in case a vocal chart with no actual vocals makes the game misbehave.
2. When I go to add new custom it asks for the download URL. The best thing I can think of is using Google Drive, but how do I upload it to look like the ones that have the dl.c3universe.com URL download template?
While you are welcome to link to customs on Google Drive, Mediafire, or any other such download service, C3 Universe is actually not a template for creating download links, but actual free space for authors that also gives you cool download statistics, both for yourself and for the community at large. If you haven't found it already, the C3U login page will tell you what you need to get into C3U, and then once inside, the FAQ will help you get familiar with the place. Note that you won't be able to upload customs to C3U immediately; as Nene~Chan mentioned, you'll have to request space first. While logged in, when you click on your name in the upper-right corner, you should see a link to make the request. Note again that you'll be expected to have a custom available for download somewhere else first, so that the C3U admins know you're being serious about authoring customs.