Q1: I'd try to use the same deployment process as used for other artifacts in my company. For example, if a deployment utility is used to deploy applications, use the same method to deploy SSIS packages (if possible).

Q2: This is a question that raises debate among most SSIS folks. Some love the file system, some love msdb. You need to find what works best for your organization. There are plusses and minuses to both. I tend to lean toward the file system, but I'm not anti-msdb.