I don't know what your tree looks like, but on a general note this should work.

Using for loop;

for i in SRP003329/*/*.sra; do fastq-dump -A $i ; done

Using GNU-Parallel

# replace the j with number of free processors in your computer
parallel -j 5 'fastq-dump {}' ::: SRP003329/*/*.sra

I don't give the output file name, it automatically takes care of it, produces file name with .fastq extension but same name.

Sounds like you just need to learn how to do shell scripting. Perhaps changing to that directory and typing the following will work:

for /D %%d in (*) do ( 
    cd %%d
    for %%f in (*.sra) do (
        fastq-dump %%f
    )
    cd .. 
)

You should, of course, change the fastq-dump command to whatever exactly you need. BTW, your life is going to be more difficult if you stick to windows. You'll find much of this sort of thing to be less clunky on Linux and Mac OSX.

Create a notepad file and open it. In the file, write:

FOR %%x IN (X:\sourcepath\*.sra) DO (X:\SRAToolkitpath\fastq-dump -O X:\destionationpath %%x)pause

Save the file. Change the file extension from ".txt" to ".bat".

Run the windows cmd with administrator rights.

In the cmd, go to the SRA Toolkit folder, where you should also have the .bat file you just created. Once in the SRA Toolkit folder, run the .bat file by typing its name and hitting "enter" (be careful with spaces and stuff in the filename).

You can customize the settings of the fastq conversion by specifying between "fastq-dump" and "-O X:..." (check the SRA Toolkit docu for details).