I want to be a little clear about something - when you say that you have the first baffle glued up - what do you mean by that? Did you not glue up the entire speaker at once? If so, you're probably going to have some problems. Any time you have a complex cabinet like this, you can't glue up in stages - things will not line up properly. In any case, what's done is done right now - I hope that you don't have any of those issues going forward.
In response to your actual question - yes, that is the way you would clean up the variance where the front baffle meets the side wings on the outside. Use the orbital sander but keep it moving - never stop in one spot to handle a particularly high area. If you're talking about where the braces are slightly protruding on the back side the best way to handle stuff like this is with a hand plane. Using a hand plane on MDF is a bit odd, but it does work and will create nice crisp cuts instead of a sander which will dish areas out. If you don't have a hand plane, the next best way would be to use sandpaper with a sanding block - trying to keep the sanding block as flat as possible. This is much more time consuming than a power sander, but won't result in any damage. Lastly, you could use the orbital sander, but be extremely careful. The pads on an orbital sander are slightly soft - so it will round things over and then start to dish out things on the sides of what you're trying to flush trim.
