How to add a Web Part Zone to a SharePoint wiki page

from: http://office.microsoft.com/en-us/sharepointdesigner/HA101513941033.aspx

Insert a Web Part zone

1. In Office SharePoint Designer 2007, open the page where you want to insert the Web Part zone.
2. If the Web Parts task pane is not already open, open it by clicking Web Parts on the Task Panes menu.
3. In Design view, click the location on the page where you want to insert the Web Part zone.

4. At the bottom of the Web Parts task pane, click New Web Part Zone.

   The new Web Part zone is inserted on the page. ...

You could also deploy your page layouts as an individual feature rather than creating a whole site definition. That way you could deploy your page layouts to any SharePoint publishing site. If you are using VS 2010, start with a SharePoint Module project. Add your layout aspx file to the project. Modify the elements.xml file to resemble this:

<?xml version="1.0" encoding="utf-8"?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
  <Module Name="Page Layouts" Url="_catalogs/masterpage" RootWebOnly="True">
    <File Path="Page Layouts\Layout1.aspx" Url="Layout1.aspx" Type="GhostableInLibrary" IgnoreIfAlreadyExists="True">
      <Property Name="Title" Value="My Layout 1" />
      <Property Name="ContentType" Value="$Resources:cmscore,contenttype_pagelayout_name;" />
    </File>
   </Module>
</Elements>

This deploys your layout and makes it available as for new publishing pages. Now, to get a webpart to be instantiated in new pages, you modify the <File> element with the webpart definition. For example, I could define a content editor webpart to be created on new pages in Zone1 like this:

<?xml version="1.0" encoding="utf-8"?>
<Elements xmlns="http://schemas.microsoft.com/sharepoint/">
  <Module Name="Page Layouts" Url="_catalogs/masterpage" RootWebOnly="True">
    <File Path="Page Layouts\Layout1.aspx" Url="Layout1.aspx" Type="GhostableInLibrary" IgnoreIfAlreadyExists="True">
      <Property Name="Title" Value="My Layout 1" />
      <Property Name="ContentType" Value="$Resources:cmscore,contenttype_pagelayout_name;" />
      <AllUsersWebPart WebPartZoneID="Zone1" WebPartOrder="1">
        <![CDATA[ 
               <WebPart xmlns="http://schemas.microsoft.com/WebPart/v2">
                <Assembly>Microsoft.SharePoint, Version=14.0.0.0, Culture=neutral, PublicKeyToken=71e9bce111e9429c</Assembly>
                <TypeName>Microsoft.SharePoint.WebPartPages.ContentEditorWebPart</TypeName>
                <Title>Content Editor</Title>
                <FrameType>Default</FrameType>
                <FrameState>Normal</FrameState>
                <Description></Description>
                <Height />
                <Width />
                <AllowRemove>true</AllowRemove>
                <AllowZoneChange>true</AllowZoneChange>
                <AllowMinimize>true</AllowMinimize>
                <AllowConnect>true</AllowConnect>
                <AllowEdit>true</AllowEdit>
                <AllowHide>true</AllowHide>
                <IsVisible>true</IsVisible>
                <DetailLink />
                <HelpLink />
                <HelpMode>Modeless</HelpMode>
                <Dir>Default</Dir>
                <PartImageSmall />
                <MissingAssembly>Cannot import this Web Part.</MissingAssembly>
                <PartImageLarge>/_layouts/images/homepage.gif</PartImageLarge>
                <IsIncludedFilter />
                <ExportControlledProperties>true</ExportControlledProperties>
                <ContentLink xmlns="http://schemas.microsoft.com/WebPart/v2/ContentEditor" />
                <Content xmlns="http://schemas.microsoft.com/WebPart/v2/ContentEditor">
                </Content>
                <PartStorage xmlns="http://schemas.microsoft.com/WebPart/v2/ContentEditor" />
                </WebPart>        
        ]]>
      </AllUsersWebPart>
    </File>
  </Module>
</Elements>

This should be more practical than creating a whole new site definition. Hope this helps.