Okay, personally I feel it's much better to write the ms with a specific target in mind. Really, there's such a difference between each line that, IMHO, it's best to have a good idea of what you want the book to be before you write it.
Let's face it, the same plot stuff can be found in most of the lines. Let's take a secret baby story. You can find a secret baby story in any of the lines -- it's the execution of the story that makes it fit one line or another. (In a Love Inspired, you'd include the faith element but no sex, in Desire, plenty of steam, in a SSE, you'd focus closely on the H&H and the impact on them, in a Super, you'd pull out a little more and include more secondary characters, more community stuff, in an Intrigue there'd be a big suspense thread that relates to the secret baby and H/H, etc.) And that's why I think it's generally best to have an idea of where you want it to go as you write.
Word counts also vary, so again, knowing what word count you want to hit makes it easier in deciding how you execute the story.
There is some overlap where lines are sort of close, where you might be able to have a story you wrote for one line be tweaked and fit at another line. (My first book for example, at first I thought was a SSE, but then discovered Super was a better fit for my voice and the types of things I liked to do with my stories. Those lines are close. Tweaking to change my ms to more of a Super was fairly "easy." )
As always, this is just my OPINION, and your milege may vary.
Susan G.