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When using the built in designs, you can click the "Customize" button to explore all design and layout options. If you need more control over the design or layout then you'll want to create a custom design template. (Templates —> Designs)
The PDF version should look the same as what you see in your browser. If the layout seems broken this is likely due to content that was copied and pasted through MS Word, Excel or a similar source. Click on the "source" button in your proposal sections and make sure there aren't extra tags or characters that don't belong there.
These proposal designer feature has been rewritten and no longer supports these older designs. Your old proposals will display using those old designs, and all of your data remains the same. All future proposals will need to use the new proposal design templates.