Atlas - first off, welcome to the forums.
You will find a vast amount of help exists here - both in terms of posted material to read, and form actual people.
Now, I'll suggest you take a minute to try out the "Search" functionality of this forum. It will be your best friend for the fastest answers to questions. Suffice it to say that chances are good anything that comes to mind will have already been asked.
This shouldn't stop you from posting up, however, as each situation is individual, and different people learn in different ways - just saying the Search function tends to be under-utilized by folks and it can really speed up your search for answers.
Next up - please define the following:
Currently I'm paying an ad agency to put me in the top three,...
Is this an "ad agency" or a search marketing company?
Does "put me in the top three" refer to submitting to directories and such or to getting you rankings in the organic search results (aka - SERPs - search engine results pages)?
If you don't know the answers directly to those questions, don't worry - just post up and we can walk you through it all.
Next, I'll suggest if this agency is being paid to "submit you to the search engines" that you stop immediately - a website does not get "submitted to search engines" and anyone selling this service is taking advantage of clients, IMO.
Also, please be sure to update your signature here with a link to your website so folks know what to reference when they're offering help.
Finally, I'll suggest picking up a book such as Search Engine Optimization For Dummies
. Some might not agree with me, but I think it's an easy read, explains the basics well and tells you the different between what's a good idea and what's a bad idea - much needed info for new folks, IMO.
So, there are some places to start.
While my book suggestion focuses on search optimization, keep your eyes open (in these forums) for ways to learn more about media buying, pay per click advertising, e-mails, sponsorships, etc. as forms of advertising for your site.
I typically start folks down the SEO road because it takes time, and not money when compared to other forms of online advertising. If you've got the budget, by all means jump into PPC (slowly) and ad buying.
Just make sure you account for a few things no matter the direction you go in:
1 - do you have actual analytics in place to measure results? (Open an Adwords account, get a small campaign running with one ad for 420 - $30/month - this will open up access to Google Analytics (if it's not already totally free for users). Install their code and you'll start seeing actual analytics about your website - a "counter" on the page is NOT analytics.
2 - Set some goals - know your limits in terms of ad dollars and make sure you watch the stats to see if you're on track to meet your goals - be realistic about everything. A new website will take a while to develop traffic, so don't be discouraged - just keep working at it.