IRCC only wants a clear and legible copy of the biographical data page of a passport or travel document. However, the MyCIC upload window asks for a scan of all valid and expires visas and markings. It does not matter that the markings are not clear.
This is confusing, so ideally you should just list all travels, irrespective of whether they were outside COR or COC. So what you did is fine.
Any person in your organisation can issue a letter it does not have to be your immediate supervisor. IRCC clearly states:
a reference or experience letter from the employer, which
- should be an official document printed on company letterhead (must include the applicant’s name, the company’s contact information [address, telephone number and email address], and the name, title and signature of the immediate supervisor or personnel officer at the company),
- should indicate all positions held while employed at the company and must include the following details: job title, duties and responsibilities, job status (if current job), dates worked for the company, number of work hours per week and annual salary plus benefits