1. I don't know that answer to this; I've installed a number of apps including Aldiko and Cool Reader, and never encountered any that flashed and did not start. Did you reboot the Nook and try again? Perhaps someone else can help you. A great resource for all things rooted is the xda-developers
http://forum.xda-developers.com/forumdisplay.php?f=1198
I've found them knowledgeable and willing to answer questions.
2. There are various ways to install apps. If you can't simply install them as you did Aldiko, but rather have them on your pc (many apps can be found on the internet that can be downloaded to a computer), then I've found it easiest to install appinstaller.apk from google play. If the apps are on your pc, then download the app on your pc that you'd like to install to the sd card and run appinstaller - the app is installed. I started with a newly formatted 4 gig sd card because I load the ebooks on my pc to the nook sd card using the usb cable, but the card does not need to be erased. Before you disconnect the Nook, be sure to eject it via Windows Explorer or like program.