When buying ships I'd highly recommend looking at Ebay for some cheap deals.
IIRC the main box set contained not only all the materials needed to play the game but 5Imperial ships and 4 Choas Ships and was priced £50 for the
UK (
US I don't know) so that should hopefully give you a price comparrison when looking for deals on Ebay.
Also, if you did manage to get your hands on the box set then as long as you painted all the ships up in the same scheme then I see no reason why you can't use both the Chaos ships and the Imperial ships as the same army. That will allow you to play as both Chaos or Imperial without having to buy additional ships. When you play as Imperial you'd just have to assume the Chaos looking ships are simply pre-heresy ships still under loyalist control ... and if you play as Chaos then the Imperial ships could simply be captured ships or the crew corrupted by choas. Either way, as long as you are happy with different styled ship with a single colour scheme then I don't think others will have an issue either, especially if the weapon systems are clearly displayed.
Additionally, check out this link if you haven't already, it links to
GW and all the free additional resources they've posted on their website.
http://www.games-workshop.com/gws/content/article.jsp?catId=cat480005a&categoryId=1100007§ion=&aId=4300022
Found this link for when
MGS was looking for info, would be worth a look for when deciding what ships to build for Imperials
http://www.dakkadakka.com/dakkaforum/posts/list/318009.page
Also this link for a Tactica of sorts
http://www.games-workshop.com/MEDIA_CustomProductCatalog/m1300008_BFG_Admiral%27s_Tactics.pdf_
At this point I'd say it you'd be best looking at other people's threads for info on armies and such, its already been asked 30times over so there is plenty of info out there, and then if you have any specific questions we can help with that. the Search feature might turn up some useful info but this little lot should give you some food for thought at least
From my own personal experience Choas tend to have greater long distance firepower whereas Imperial have superior close quarter firepower, Imperials also have the ability of choosing torpedo salvo's or the devastating Nova cannon whereas the Chaos can only choose front Laser batteries. In truth both have pro's and con's and it depends on the situation your in. Having chaos with front Lasers might seem best, but being able to use torpedo's to help channel the enemy in a certain directions is equally useful.
I still think buying the main box set is your best bet, and if you really don't like a certain army after you've tried them from either looks or a gameplay perspective then you should be able to sell the opposing army on Ebay or to a friend, etc