Generally speaking, ocean objects go on a layer that is underneath the land layer, where lakes need to go on top. (Layers get rendered in the order in which they appear on the list, top to bottom.)
If you hide the land layer(s) until the land disappears, I suspect you'll find your lakes underneath. Then you can move them to a different layer that's below (on the list) the land layer. (You might want to create a layer for that, or there might be one already there that's suitable.)
You have to be sure that lakes go on a sheet lower on the list than the land sheet. The sea fractal polygon you are using is probably set to automatically go to the background or sea sheets near the top of the sheets list, so the land would hide them. You need one below the land sheet (its actually upsidedown -- those sheets higher on the sheets list are lower in your map -- the map draws from the top down, each subsequent sheet going over the one before it).
Most map styles have a lake tool, precisely to get the sheets correct. If it is fractal or smooth depends on the style (Some have both). Using the sea tool is fine too though, it is just that you need to fix the sheets manually after placing it like explained above.
If, for some reason, there is no lake tool, you can quickly make your own. The easiest way might be to save the sea tool with a different name (e.g. change "sea" to "lake") and then edit the newly-saved tool to use the RIVERS sheet, LAKES sheet, or some other sheet that sits above the land. For details how, see Monsen's excellent Command of the Week series posts, Managing Drawing Tools (Week 20), and Automatic Sheets for Symbols and Drawing Tools (Week 46), and/or read the informative Drawing Tools section in the CC3+ User Manual, starting on p. 86. It includes sections on editing and creating drawing tools.
Comments
If you hide the land layer(s) until the land disappears, I suspect you'll find your lakes underneath. Then you can move them to a different layer that's below (on the list) the land layer. (You might want to create a layer for that, or there might be one already there that's suitable.)
What I do is this:
sheets
Sea
land
lake
symbols
text
Sea gets drawn first, text is last.
Cheers,
~Dogtag