In many cases when I do a stock sale, the transaction is reported on my 1099 as multiple transactions reflecting how my brokerage split the order. For example, assuming I sold 1000 shares of CompanyA, since I didn't have a "All or None" order specified, my brokerage sold the shares in lots of 400, 400 and 200. So, I get one single trade confirmation for 1000 shares, but the 1099 shows it as three gains.

When I enter this information on my Schedule B, does IRS require I enter three lines for each of these lots (although they are the same trade) or can I just enter one for 1000 shares ?

Essentially, does IRS care about the number of transactions matching the 1099 or does it care about the final amount ?

Yes, one entry for 1000 shares sold (if you doing it manually)
Some brokers let you download the stock sales transactions directly to the tax software.