Do you have it added to your startup-sequence/user-startup ? It needs to be there (and placed correctly) with correct arguements following, otherwise you'll need to manually launch it everytime. By the way if you're an rtg system with '060 (or higher speed(ie. emulated)) I recommend using AFA_OS instead. It's skinning system is more flexible and it also adds other functionality too (anti aliased fonts, 32bit png icons, faster icons, zune, etc.).
p.s. Startup sequence and user startup rock. You just need to understand amigaos a little to use it properly. Also, WBStartup is handy, but not half as flexible. Birdie is a command line program, thats why you need to add arguements and why you cant just place it in WBStartup.
Startup-sequence and user-startup are very simple and easy to use, no other system lets you so easily customise your system. And for the record, yes even Mac OS, etc need to be told where everything is, it just hide it from the user unless they care to look for it. Personally I like having complete control over my computer and not have it assume Im stupid.
As for birdie if you want your arguements for birdie, just check open up the birdie file in env and it'll give them to you. Basically though its a 3rd party system hack, if you want to use things like that then you need to learn AmigaOS a little. Whinging because of your lack of knowledge isnt the best way to get help.