How will the success of my previous projects affect future funding? I have two funded projects. One works great but the other is terrible (probably wrong postdocs and PhD students). When I send future proposals, my history is evaluated against the overall research output, right? There is no factor indicating one of my projects has failed, right?

I have two options:


Let the weak project fail and focus on the successful one to improve my overall research output. Then, I have a strong record of publications for the future proposals.
Use some funds from my successful project in the problematic one (e.g., hiring more people) to save it at the cost of sacrificing the successful one.


By the way, I am an assistant professor of chemistry (close to promotion) and the projects have been funded by European schemes, if it matters.
While a common practice, that would be fraud. 
Less fraudulent would be to bill everything that 'counts for both' to the stronger project, to conserve money to get the weaker projects done. (Equipment, staff meetings, etc). 

For you, depends on how your department weights grants brought in vs. papers published. If they value grant money more, that you've damaged your chances of getting more is not something your should reveal, while papers are something you can play up.