This is pretty simple.
You do not need to use AutoIT for this.
So, I assume that you have list of ID, that will map to a folder and those folders has list of excel files that you need to upload to a website.
You can divide this into two parts.
Part 1.) Search Excel file
Part 2.) Upload the file to a website.
Part 1:
First you can write a program to list folders. Say, you have got 10 IDs (this can be dynamic as well). So, you have go 10 folders mapped.
You can store this list of folders into List<String> variable.
Now, you can iterate through List<String> and get a list of excel file from each folder and store it into List<String> variable.
If you want to map retrieved excel file with the ID, you can use HashMap<String,String> as well.
So, you have got list of excel files mapped to the ID.
Part 2:
You can use framework like Selenium(https://www.seleniumhq.org/) to automate the file upload to a website.
Hope that is clear.