When you're used to having only one account logged in an app at a time, concern that you may impact your main account by having a second one via Multiple Accounts is definitely understandable! The good news is no, having a second account in any app will not affect your primary account.
This is because Multiple Accounts creates a clone of that app and runs it in a separate instance of Android. The result is that the two apps run simultaneously and never share an environment, which means they'll never interact or cause an issue for the other copy!