Its up to you, but I always prefer to start off with a full score of, say, 16 staves rather than a short score of 2 or 4 staves. Thus if the tune in my head is for, say, the flute, I can write it for that instrument straight into the score. No doubt non pianists such as Spohr and Berlioz would have done the same.
For a good number of years I used Noteworthy software, which, at $49 a go, must certainly be one of the most reasonably priced Score writers on the market. Its also one of the easiest to learn to use and is well backed up by a good friendly newsgroup and forum. However, I have lately moved on to the much more powerful and expensive Sibelius software which can to do lots of things that Noteworthy cannot do, such as copying and pasting large chunks of score. To accomodate the necessary numbers of staves for a full orchestra it is usefull to have a computer monitor that can be used in portrait mode.
As for textbooks on orchestration; I can thoroughly recommend Berlioz's magnificent "Treatise on Instrumentation", but I also find much usefull information in Gordon Jacob's more concise "Orchestral Technique"
Personally, being a bit old fashioned, I tend to use as my models.various early to mid 19th Century symphonies by Beethoven, Schubert, Spohr, Lachner, Kalliwoda and Raff.
Best of luck,
John.