I spoke with the reigning expert on Van de Velde drawings, and we discussed English 5th Rates. We can't make any blanket assertions that apply to all ships, but we can make some generalizations.
Most 5th Rates, from the 1650's and 1660's, had forecastles. One prominent exception was the Garland.
Perhaps all 5th Rates had two decks. Only the lower deck was completely armed.
Generally, the upper tier had guns under the forecastle and under the quarterdeck. There may have been ships where there were guns under the ladders. A few ships had guns on the quarterdeck,. such as the Speedwell.
I will be modifying my 5th Rate drawings, accordingly.