so, I think that I have some insight into these issues.
The first one has to do with flex. flex allows us to have a linked folder outside of the main workspace folder. if I open one of these files that is outside of the workspace folder (but in the workspace), bookmarks dont work.
If I do the same with a file that is in the actual workspace folder, it works fine. also, I noticed that the typical eclipse project doesnt allow files that are outside of the workspace folder to be included in the workspace without copying them over.
So, it looks like this is an eclipse deal, or somehow if I open a file from slickedit or the file system, somehow, I have to reroute it through the flex view or do something similar to what the flex view is doing.
the other issue is with associating an untitled text file with slickedit. For this, it looks like the only way to do this, is to rewrite their UntitledTextFileWizard and force it to open slickedit instead of choosing the default editor (which always comes up as the default eclipse editor because of a missing file extention). it looks like there is a line of code there that allows me to do it. instead of rewriting their wizard, I guess it's possible to add a custom "scratchpad" file wizard these changes.
Both of these issues are kind of low priority for me, getting the debugger running is my number one issue right now. As it is, I am starting to rely on traces instead of stepping through code. Have you tested support for the flex debugger with slickedit? is this something that should work? if it's not, then I might need to find a way to set the default editor to the flex editor when going into debug mode, reopening all files in that editor. and doing the reverse when exiting debug mode.