Converting PayPal CSV
CSV files from PayPal should be mapped automatically by default. Please send the file you are trying to convert (you can leave the header and few lines from the file, the whole file is not required).
PayPal files usually have a net amount, gross and fee amounts, and when QIF and IIF formats support splits, QBO/QFX/OFX files do not support splits. CSV2QBO, CSV2OFX, CSV2QFX can create separate transactions for gross and fee amounts, which is what usually users are looking for.
Please use the latest version ( start existing one and select Help->Check for updates and update).
If you have a manual mapping applied, select [auto]. You should see split1 (gross), split2 (fee) columns filled. For non-zero fees, CSV2QBO/CSV2OFX/CSV2QFX will create a separate transaction on the QBO/OFX/QFX file, which you can assign to another expense account in Quickbooks/Xero/Quicken.