I'm mixing and matching some of the smithing mods out there. I was wondering:
1. Is there any way to copy multiple entries from one record to another. (Holding CTRL and clicking doesn't work.

)
I assume you mean groups ("GRUP (COBJ)") whenever you say records ("COBJ"), right?
You can copy whole groups if you want to copy all records within, and you can work quite quickly using Ctrl+C and CtrlV, even from one TESsnip window to another. But there are no multiple-select options I'm aware of.
If you actually meant subrecords when you wrote "entries" then no, you need to use "Edit / New Subrecord" to add new ones (and you really need to know what you're doing.
2. Is is okay to have multiple instances of a single record in the esp? Like Two COBJ records, but each record has different entries. (I'm guessing that's a no, but it would make this process swifter. But I do have to check the form id's anyway....)
The system is very tolerant about such things even if records are in no group at all, but you should always try to create a proper file.
Use "Spells / Sanitize" to put everything in proper groups and combine multiple goups into one.