You have just set up yum access to four different repositories. Before you go further, you need to know that mixing RPMs from multiple repositories can be a chancy business; sometimes they can conflict with each other, or have different and incompatible dependencies.
The livna.org people take particular pains to track what Fedora is doing, so you should be safe there. The MPLUG site is also pretty safe; they only supply one piece of software which depends mainly on the rather stable Mozilla plugin interface, and downloading an out-of-sync version of flash-plugin probably can't do anything worse than stop you being exposed to Flash animations (many people would actually consider this a feature).
The FreshRPMs repository, Dag Wieers's site, and any other "outside" sites are potential trouble. Their maintainers work hard at providing a useful service, but for various technical and political reasons they don't coordinate with Fedora as closely as one might wish. To avoid problems, I recommend the following precautions:
Installing or updating particular named packages with apt-get is OK, but don't do a general upgrade using it. Use yum or up2date instead. (None of the procedures in this HOWTO use apt-get.)
Disable apt-get access to any site that you have yum or up2date access to. This may help avoid database inconsistencies. (None of the procedures in this HOWTO use apt-get.)