How should I complete the remaining income tax related formalities?

I am salaried and TDS is deducted by my employer. However I failed to inform my employer about income through fixed deposit and savings bank interest (which is taxable though not of large amount in my case.) Can anybody please clarify my doubts regarding filing of IT return? So far I had taken help of one expert about this but this time I want to do it myself through e-filing.
1. Can I deposit the extra tax (self-assessment tax) to the government through my internet banking facility of savings bank account?
2. Earlier I failed to take into account correctly a few deductions from income and so some extra tax had been deducted by my employer. Can I now myself correct this and obtain the right amount of tax to be paid and then deposit the same through above procedure?
3. It seems there are two ways of e-filing, one is to follow IT department of govt of India and the other is to use help of some websites. Which one is better for some one like me (without any experience of e-filing)? It is compulsory to print ITR forms in colour printer (my printer is unfortunately black-and-white)? I have asked too many questions and I thank anybody willing to offer a little help.
Further clarification needed!!!
I just checked the form 26AS and was surprised to note that my TDS is not shown. I am sure this had been deducted by my employer; may be they are taking time to put it on the web. But the question is will I be allowed to complete the e-filing process with the current status of 26AS?
I thank Max for his detailed answer.

How to invest in Indian Mutual Funds Online?

I am looking for an easy way to make investments in the best performing mutual funds from India.
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Can anyone let me know how can I buy/sell or purchase mutual funds units online and manage my investment solution completely online?