Galaxy specific questions are best asked on their dedicated support forum: https://help.galaxyproject.org/

Are you interested in moving all .fastq files from various folders into one? Because that can be done with a single command, but not sure that is what you want.

am unable to insert all seperate datasets into one big folder. 

Doesn't make sense as Galaxy doesn't use folder concept. Instead, it uses datasets, collection lists, collection list of pairs (AFAIK). Probably you meant a single list or single list of pairs.

1. Create a history
2. Switch to the newly created history (from step 1) if some other history is active
3. Download the datasets (data) from URL (web) or from local machine
4. Now you should see all the imported data in that history
5. Create a collection with downloaded datasets ( data from step 3). It would be either lists or paired lists depending on the datasets
6. Run the tool on this collection. This would run a single tool on all the downloaded datasets.

5th step is important. Make sure that the tool takes the lists of datasets (collection).