Usually all the plugs come out. However, there are plugs on the pump, filter and other equipment that need to be put back in before firing up the filter.
I doubt you can do any serious damage trying to open the pool yourself - if you have any trouble, we're here to help you and, if push comes to shove, you can always call in the pool co. (they should cut you a break on price for already having removed the cover)
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