Your company will have produced take-off performance data for the airfields you operate from. These take-off weights are derived assuming you will follow the engine out procedure in case of an engine failure, therefore yes, you always follow the engine out SID unless you have a compelling reason not to.
In the case of a missed approach you use the published missed approach for the approach you are doing. Once again your company should have produced landing data that gives max landing weights assuming you will follow the published missed approach. In some cases you might have to use a higher DA/MDA in order to meet the missed approach obstacle clearance requirements. All of this should be spelled out in the company's performance manuals.