If you run an s.r.o. company in CZ, the rules for VAT are same as for the trade license holders. The big difference for the s.r.o. is that you need to keep double-entry bookkeeping, which usually requires a professional accountant and often the use of accounting software. The profit of an s.r.o. is taxed by 19% of the corporate income tax.
If you want to “distribute” this taxed profit (it means to use the profit for your personal purposes), you need to pay 15% of the withholding tax up to 19%. The taxable period is also one calendar year with taxes due by March 31. You need to prepare a year-end financial statement (which includes a balance sheet, a profit and loss statement and footnotes).