I have used PayPal and found it to be a great process. You can send an invoice with the PayPal link and the client pays from that.
As far as the fees, I believe they can be written off as a business expense. I would ask your accountant to confirm if this is fact.
If you are invoicing $10.00 through PayPal the fee would be about 60 cents. If you figure this is the way you will bill all your invoices you can estimate for the year and then factor that in when you are figuring out your rate.

Debbie