I've found that if you read the pamphlet, fill in the form as best you can, and write a covering letter with the form which explains what you have done and why, then IRD are very reasonable and helpful. In my experience when I've done this I have always ended up paying less tax than I actually thought I should be!
The reference document for how salaries tax is calculated on provision of a place of residence is this one:
http://www.ird.gov.hk/eng/pdf/pam44e.pdf
Essentially, if your employer provides a place of residence for you then it has a taxable value of 10% of the rest of your income for the period for which it was provided. So if, for example, your employer provided a residence for the first 3 months and during those three months your total income was, say, $300K ($100K/month) then the taxable value of the provision of residence would be $30K (10% of $300K). If you earn enough to be subject to the flat rate of tax (16% this year) then the tax payable on the place of residence would then be 16% of $30K, or $4800.
