Hi Sherwin,
Yes its true that only works for content pages. What you should do is in your custom page is setup your own column layout all inside the center column so it doesn't depend on the master page managed layout for other columns.
One simple way that may work well enough for you is to use some built in style (floatpanel class) we already have like this:
<div class="floatpanel">
<asp:Panel id="pnlColumn1" runat="server" CssClass="floatpanel">
<h2 class="moduletitle">Column 1 Heading"</h2>
... more content
</asp:Panel>
<asp:Panel id="pnlColumn2" runat="server" CssClass="floatpanel">
<h2 class="moduletitle">Column 2 Heading"</h2>
... more content
</asp:Panel>
</div>
You can add as many panels as you like but if they don't fit they will wrap, which is actually more gracefull than requiring scrolling. Wrapping them all inside another div with floatpanel class helps with some IE issues.
Hope it helps,
Joe