When exporting from Motion, we are presented with a lot of choices. This is great as it allows us to export for many different situations and needs. The down side of this is that for the new user it can be confusing. Here I'll do my best to simplify things.
We talk about alpha channels in motion graphics and effects work a lot. For those who don't know, I'll give a brief explanation. A regular video or still image is a solid thing, what you see is it, you can not see through it, it is not invisible at all. An alpha channel is metadata about our video or still image that is tagged as being invisible. So if I put a clip in my FCP X Timeline, and a clip with an alpha channel attached above it, the part of the top clip that is assigned as alpha channel will be automatically invisible, showing the clip below it. The parts that are content and not alpha channel will show up, and you will not see through it to the clip below at all. A good example are titles in FCP X. When you apply a title, only the text covers the clip below. The rest of the title clip's frame is invisible, so you can see the image below it. That invisible area that is not text is an alpha channel.
With a Motion project opened, the first thing to pay attention to is the project settings. The very top layer is the Project Layer. Select this and F1 to the Properties pane. Towards the bottom of the General section is a menu for 'Background'. This determines the 3 levels of how the background is handled. 'Transparent' means no matter what background color you select, it will not be included in your export, it will not interact with other elements in the Canvas, there will be no alpha channel. 'Solid' means that it will be included with the export as a solid alpha channel, but only if you chose to include an alpha channel upon export. The alpha channel will be any area inside the frame, that is visually present in the Canvas, as the background color only. 'Environment' means it will do all of this and will interact with other elements in 3D groups.
In the Canvas at the top right is a Render menu. Here we can control what happens in the Canvas while we work. I mention this because we have to make decisions about these same things when we export. The rule of thumb is to turn off everything you're not using such as shadows, lights, etc. when you are not working with them, or don't need them. You can also downgrade the image quality in the Canvas for more complex projects to get better playback performance. These only effect what you see, how you see it, and how Motion plays back for now.
We have a Share menu in Motion, very similar to FCP X, except that it is in the menu bar up top. Normally you will export, or 'Share' using the 'Export Movie' option, or Command-E. There are many other options too, and they are pretty self explanatory. I want to concentrate on the Export Movie option, as that will be used the overwhelming majority of the time, and my space is very limited for this article. But here is the URL for Motion 5's online user manual about exporting if you want to go deeper.
Once the Export Movie option is selected we are presented with an export settings window. Here we get to the heart of the matter. There are three tabs: Options, Render, Summary. In the first tab, Options, we can select how our export is handled. Export allows you to select the codec you want to export in. The choices are any flavor of ProRes, Uncompressed 8 or 10 bit, DV, DVCPRO50, and three flavors of IMX. For this article we will stick with the ProRes flavors. If you're going to another app to use the project as a simple video clip, use ProRes 422. If you need higher resolution for some high-end app for theatrical release on large screens use ProRes HQ. If you need your project to carry the alpha channel for use in compositing use ProRes 4444. It really is that simple.
'Open With' tells your Mac what to do after the file is exported. Do you want to open it inside of another app for more work, or in QuickTime Player to preview, or none at all?
'Include' simply tells the export if it should use only the video content, or add the audio content with it. A word of warning, Motion is a tiny bit weak handling audio, so you may want to only export the video content, and add back the audio in something like FCP X or QuickTime Pro.
'Duration' is pretty simple, also. Do you want to export the entire duration of the project, or only what is in between the Start and End playback markers in Motion's timeline?
The 'Render' tab can look overwhelming at first glance, but it is really pretty simple. The first setting, Color, lets you select to export Color, Alpha, or Color + Alpha. Color is the video content only for use with FCP X or some other app using the export as a simple video clip. Color + Alpha includes the alpha channel BUT only when you've chosen a codec that supports alpha channels in the Options tab. ProRes 4444 is the best option to use here. Other ProRes flavors do not support alpha channels. Selecting Alpha only is a higher level operation I won't detail here due to space limitations. Again, see the user manual for more in depth info about this.
Render Quality, Fields, Motion Blur, Frame Blending all override these same settings in the Canvas' own Render menu. Thus you do not have to reset all of these in the Render menu before exporting. You can export a high rez version and go back to working on your lower rez version in the Canvas right away, without resetting two sets of parameters.
The right side has 3D Rendering settings. These ONLY work if you have 3D groups with 3D content in your project AND have an active Camera in the project. Otherwise these settings are ignored. Again, these override the same settings in the Render menu in the Canvas.
The 'Summary' tab is only a way to review your export settings at a glance. There is some valuable information here. I recommend to my students to always look this over before clicking the 'Next' button. It will show you the estimated file size, codec, frame dimensions, frame rate, all of the things that are vital to know before you do the actual export encoding operation. Simple, but vital.
For the season user all of this exporting information will be second nature, but for the beginner it can be overwhelming. My goal for this article is to help the beginning Motion user to understand easily how this all works. The most important thing to remember is that before you export (or before you start the project at all), be sure you understand in detail what the requirements of your exported video clip needs to be. Alpha channel or not? The whole project or just a small bit? Once you know clearly what the specific needs are for the exported clip, the rest will be quite easy... now that you've read this article.