Welcome to WebmasterWorld Kirky!
Will it negatively affect the company site if I duplicate content onto my boss' blog and link back to the company site?
They are on different domains?
There's a lot of confusion about duplicated content - search engines took a dim view on it because people were producing MASSIVE amounts of content for spam.
But legitimate uses like you're suggesting isn't an issue in terms of "negative" impact. However, there is an issue of "diluted positive" impact.
Generally with blogging you do it because you want people to link to you - but if you have the same content on two sites, some people might link to site A and others to site B, so the overall impact is diluted.
So while there's no negative risk, it might be worth assessing whether or not the dual blog approach is the best strategy. If it is, then there are other ways to manage it (i.e. promoting your boss as an individual "brand" via the corporate site instead of simply mixing in his posts with others).
Certainly, I wouldn't want to have the exact same posts on two blogs (it would be pointless and may be interpeted as spam), but if both have their own unique focus, it might want to cross-post my best posts.
That make sense?
If I have written an article on another website is it better to link to the sub page regarding the topic or the top page of the company site?
The target of the link is less important than the intention behind it these days. SEOs may recommend deep linking (linking to sub pages) as being beneficial (and it is), but recent changes with search engines mean this area has become very complicated.
If you are basically guest posting on other blogs to promote your company, then I would start off by linking to your company homepage using your company name or straight URL (i.e. don't try any SEO / keyword linking, etc).
That's the safest way to start and it will pass on some SEO and some marketing benefit to your company.
As you learn a bit more about SEO and the issues involved in link building, you can get a bit more creative and aggressively target your keywords. The issue is if you do that without really knowing the risks, you could cause damage to your rankings rather than improve them.
But don't think that because you're taking the "safe option" of linking to your homepage, it won't be as effective. In fact you'll be building a solid SEO foundation for your site and gradually improving the rankings in preparation for "fine tuning" at a later date.
If you have any other questions just shout.