If you use ActiveSync on your Android device you are not able to sync more than one calendar. The reason is the missing support in the ActiveSync implementation of Android.
Using Android multiple calendars is not a problem at all – as long as you use Google Calendars. However, in business environments – or if you want to keep your data private – it might happen that you want to use your own calendar server. In such cases the sync is most often done via ActiveSync – and there multiple calendars cannot be synced, see for example Google code issue #36797. Of course, there are also other protocols like CalDav, but unfortunately Android does not support these natively.
There are lot of discussions out there why this does not work, and the situation is not simplified by the fact that there are various ActiveSync implementations on server side and even on mobile side (Samsung ActiveSync vs Google ActiveSync, etc.). But for plain Android, the situation is clear: the code lacks the ability.
The Exchange ActiveSync protocol specifies types of folders – like one type for the default mailbox, one for user created mail folders, etc. And while Android does know the type “12, User-created Mail folder”, it does not know the type “13, User-created Calendar folder”. It does not know “14, User-created Contacts folder” either, by the way. It’s simply not implemented in the class “FolderSyncParser”. Just check the list in line 60-75, and compare it to the above given type numbers.
Thus you are not able to natively sync multiple calendars with plain Android and ActiveSync. If you really need it, you have to use one of the many, many hacks: export to Google calendars, create one user for each calendar on the server side, etc. – or use another protocol like CalDav which is not natively supported in Android but can be added by 3rd party tools.
I do hope that Google implements multi calendar sync via ActiveSync (or CalDav, speaking about) at some point in the future. I find the feature of multiple calendars extremely helpful in the daily office routine. But then again, there would be one reason less to use Google calendars on Android phones, so it might be that this is a political decision.