There may be an easier way to accomplish what you asked for (and if there isn't there SHOULD be) but try the following procedure; it will work:
1) Begin by choosing the theme and master that you want to use for the presentation and create your first slide. Save-As: give it a name and location to save.
2) On this first slide, create your header (if you want one) and insert the graphic image of your company's logo where and how you want it to appear on all other slides.
3) If you intend all (or even most) of your slide transitions to be the same type go to the Inspector > Transitions menu and create the one you want to use. This will save you the time and trouble of doing this for every slide you create. You always can change the Transition criteria for individual slides if you want to do so.
4) In the Slide Navigator (or Light-table) window, the slide you just created will be shown. Click on it to highlight it. Then Copy (Command-C) and Paste (Command-V) as many copies as you think you might need for the presentation. Don't worry, you always can add more or delete extras as needed.
Each of the copies will have the same attributes as the first slide. Into these, you can add or change anything you want, including the slide format, but the header, logo, and Transition will be exactly how you created them for the first slide.
IF you already have created your presentation, then the easiest way to add a logo in the same place is to create it on your first slide and Copy (Command-C) it. Then, on each succeeding slide (NOT in the navigator window, but on the slide itself) Paste (Command-V) it. It will appear exactly as it is on the first slide.
Good luck.
