If you want to patent your software worldwide, you have a lot of filing ahead of you. Generally speaking, the filing needs to be done in a relatively timely manner too, so missing deadlines happens routinely. I would suggest consulting with an intellectual property (IP) attorney who can help you meet all of the necessary requirements because they can be tricky.
Filing with the patent cooperation treaty (PCT) really will only give you an opinion as to whether your software can be patented in the countries that signed the treaty. This can be helpful because searching all of the countries on your own would be troublesome. However, after the search, you will still be without a patent.
So, if you file with the PCT for an opinion first, you will still be left with all of the actual patent filing to do. You will then need to file for a US patent and then for any foreign patents that you wish to obtain. Each patent will have separate requirements.
Again, my suggested strategy would be to consult with an attorney. An experienced intellectual property attorney will be able to search for any conflicting patents and will also be able to file your patent applications for you. You will have to pay your attorney a fee, though, and I know that this is not ideal. But, it is possible to save money on attorney fees.