After a few test I can say (like others did before) that Makerware is not yet ready to be used exclusively. There is for instance a bug which prevents it to print at the highest resolutions... This is a pitty because it really is a better interface and much easier to use than Replicator G, the open source software used before. Anyway you can still use Replicator G and it works as it should. Like that I would say you should try it with Replicator G, especially if you are more experienced with 3d printing because Replicator G gives many more settings to configure your printing.
Do not wonder about the warning in ReplicatorG or the not connected sign in Makerware. It is not possible to use both at the same time, since they are using the same connection and will block each other when opened both. To get rid of that you need to go to "Services > Stop Conveyor" and like that make the connection available again.
If Makerware gets bugfixed it is a great software too. It has a better interface and some small but helpful features like a measurement tool to see how large something is, you can place more than one object in (which sounds unnecessary but is very helpful if you for instance scaled your object and want to reimport it because of some changes done in your 3d software, etc.
I am going to do some more research and will be back with infos here, if it is working in future. It is still heavily under developement after all...