Expenses are charged to or deducted daily from the fund. So if the expense ratio is 1%, then 0.01/365 of the funds assets are removed daily.
If you have a wrap-account, then additional fees are charged on top of the underlying mutual fund fees and expense ratios. You wrap account agreement should state when these extra fees are charged. We have 529 plans and they charge an administrative fee of about 0.03% every quarter on top of the underlying mutual fund expense ratios of between 0.03% for VIIIX and 0.56% for VTRIX.
The Morningstar X-ray feature will total up your assets and funds that you give and give you a total expense ratio for your portfolio. Our portfolio is at 0.6%, so I'm working to get it under 0.5%.