I don't use the input switching with My Movies. My universal remote handles all of that. I have an activity in my universal remote for Windows Media Center. I also have activities in my universal remote for each of my Sony changers. My Movies knows which changer to power on and which disc to play per the assignment I made for the disc in the Collection Management (CM) application.
So once I select the "Play" option I just change to the particular changer activity in my universal remote. An activity macro runs when I change to the activity which does the input switching. The proper source selects are made and I'm all set to control the changer. My Movies has already powered on the changer, so I just wait. Once the changer is fully powered on and at the XMB the serial command is sent by My Movies to play the disc I selected. Done deal.
This begs the question though. How do I know which changer activity I need to go to in my universal remote once I select the "Play" option? For this I key off the "Location" section of the My Movies for WMC interface as shown below. There's an option within CM you'll need to be sure you have selected for the "Location" details to be shown.

I should mention this as well. By default the "Location" details are displayed with a bunch of unnecessary canned text. The canned text precedes the actual changer name and slot number. As a result, at times some of the actual location details can fall outside the boundaries of the interface, cases where a title contains multiple discs. Even when that doesn't happen I find the canned text annoying, so I just remove it. This is done by editing the localization file for the language you're using. The localization file for English is called, "localization_1033.xml". I'm still running My Movies 4.07, but I'd imagine the localization files still resides in the same folder path. (C:\ProgramData\My Movies\Localization\localization_1033.xml) Should be pretty easy to find in any event.
Should mention this as well. Even with the canned text removed, the "Location" line item there only provides enough room to display a few disc locations, so if a given title contains more than one disc I also include the changer name and slot number in parentheses when naming the discs in CM that way when I select the "Play" option the location details are displayed right there along with each of the disc names. Example shown below.

In the above example there are 7 seasons total if you keep scrolling down. Quite often I'll create individual titles per season. I may do so for this box set eventually. Just haven't felt like it yet. Note also how I added extra discs solely for use as labels and separators. Makes it much nicer when browsing down to the disc I'd like to play with a large box set like this.
There's also a golden rule I always follow which I recommend for those with multiple changers. Never allow the discs for a given title to carry over from one changer to the next. This provides for the first of the "Location" details displayed telling you what changer each of the discs reside in for the given title. As a result, it doesn't really matter if there's enough room to display all the location details. Since the first of the location details tells you which changer the discs reside in you're all set. Once selecting a disc to play you just change to that changer activity with your universal remote and wait for the disc to play.
Now in my case I quite often won't even select the disc from My Movies. I'll just use My Movies to browse for what I want to watch. Once I find a disc I'd like to watch I'll instead select the changer and slot number using my universal remote. That's why I always ensure the changer name and slot number for each disc are prominently displayed within the My Movies for WMC interface, even if that means including those location details as part of the disc names. I provide a brief walk-through of this in a post over at AVSForum
here if you're interested in checking it out.
My DVD/Blu-ray CollectionHome Theater Gallery