I've started created my epub v3 with Sigil, should I have used Calibre instead?

I’m new to creating ebooks. I have mp3s and mp4s that I want to include in my epub so I started off making an epub v3. I started with using Sigil to create my file but I’m wondering if it was a mistake.

• I’ve opened a bunch of epubs that I already have with Sigil and noticed that they are filled with Calibre references.

• Missing meta data seems dodgy to add with Sigil. It isn’t very intuitive and I’ve been adding the fields manually in my Content.opf file.

• There isn’t any toc.ncx. Even after generating a table of contents it doesn’t create a ncx file. TOC is still empty in my epub reader (Marvin).

Perhaps I’m just new to all this, I hope my question isn’t too opinion-based or preference orientated, but would I have had an easier time with Calibre or some other software? Will I be creating issues for myself by starting with Sigil now, if I want to switch over later?