EffectsLab isn't a compositing program, so there will always be limitations as far as what you can achieve with it regarding compositing. that article details several of the tricks you can use to work with stock footage, though.
EffectsLab is only intended to composite light-based stock, such as explosions, muzzle flashes, etc. All of these are effects requiring either Add or Screen composite for convincing results. Either one of those composite blend modes can potentially create transparency, depending on the specific stock and background clips involved. Keep in mind as well, that the percentage of the time that a single layer of stock can be added to a clip as a composite without any other adjustments or layers being needed is approximately 0%. As in, never.