Well, about the missions, they tend to be easy as long as you stay around the core world of whatever empire you've chosen. And you'll usually have the backup of larger ships 75% of the time (The first time I started a patrol mission I got the Enterprise NCC-1701-A!). The same is true for borders shared with allied powers, if there are any ships in that sector they'll assist you most of the time as well. Just hang around the core sector until you've found your footing, it's good practice for what comes later in the campaign.
As for customizing skirmish levels, you can create your own with an app called FMSE[/b] (Fleet Mission Script Editor), it should be available for download from Dynaverse's download section. It's really easy to use, and great if you just want to make different scenarios/settings for a skirmish. But it can't do fine tuning, create missions and do the small details like crew conversations and stuff right. You'll have to learn to script to do that. For that I reccomend a program called "Bloodshed C++" (Just google it), it's a C++ code editing application with all the bells and whistles and can do the small stuff easily.
Hope that helps.