The issues here is probably with the task manager's reporting. Since a2sd scripts like s2e bind internal /data/app folder to /sd-ext/app folder, and thus any apps which are installed in internal memory are installed to external sd-card partition. The task manage app you are talking about is probably fooled by the script. 

So, there's no need to worry at all provided that you see your apps at /sd-ext/apps directory. If you still have doubts you can confirm that by navigating to /data/app/ directory and learning that there are no any apk applications you have installed so far. It means S2E script is working just fine and you needn't worry a thing about it.

About the used internal memory you've reported -it's so because still some data (either Dalivk Cache or Applications Data or both) are inside the internal memory card. While it is not recommend -for best performance- to move dalvik cache to sd-ext partition, you can still move applications data to sd-ext partition from with s2e app menu and reduce the use of your internal memory. There's another reason not to move dalvik cache to sd-ext i.e. We are trying here to reduce the use of internal memory not make it empty instead, which would render it useless. But, you can still move it to second partition on your sdcard if you want.