The first one is quite easy, you have [itex]\delta \dot{\phi}=\partial_{t} \delta \phi[/itex], now pat of the assumptions of calculus of variations is that the variation vanish at the boundaries. I think that will help you clear up your first problem.
Okay you have:
[tex]
\delta S = \int_{t_{1}}^{t_{2}}\frac{\delta L}{\delta \phi}\delta \phi +\frac{\delta L}{\delta \dot{\phi}}\delta \dot{\phi} d^{3} \mathbf{x} [/tex]
Using the hint that I gave:
[tex]
\delta S = \int_{t_{1}}^{t_{2}}\frac{\delta L}{\delta \phi}\delta \phi +\frac{\delta L}{\delta \dot{\phi}}\partial_{t}\delta \phi d^{3} \mathbf{x} [/tex]
The second term can be integrated by parts to obtain:
[tex]
\int_{t_{1}}^{t_{2}}\frac{\delta L}{\delta \dot{\phi}}\partial_{t}\delta \phi d^{3}\mathbf{x} =\left[ \frac{\delta L}{\delta \dot{\phi}}\delta \phi\right]_{t_{1}}^{t_{2}}-\int_{t_{1}}^{t_{2}}\frac{\partial}{\partial t}\frac{\delta L}{\delta \dot{\phi}}\delta \phi d^{3}\mathbf{x}[/tex]
Putting this back in the same integral we have:
[tex]
\delta S =\int_{t_{1}}^{t_{2}}\frac{\delta L}{\delta \phi}\delta \phi -\frac{\partial}{\partial t}\frac{\delta L}{\delta \dot{\phi}}\delta \phi d^{3}\mathbf{x}[/tex]
So you see now?
For that one, take a simple case of where the field has one space variable, i.e. when [itex]\phi \phi (t,x)[/itex] It will be easier and give you a good feeling for the general case.