[R-sig-ME] repeated measures and random effects question

[Moore, James Roy]

Hello list, 

Not sure how to address a list, so let me know if I'm doing something wrong.  

I'm having a difficult time wrapping my mind around how to account for repeated measures and random effects and was directed here.

My experimental design is:
4 sites
2 plots per site (control and treatment, 10m x 10m)
8 subplots per plot (1m x 1m) 
3 years (each subplot sampled once per year every year)

Response variable: proportional plant cover
Potential covariates/predictors: other proportional plant cover, herbivore damage
The treatment is herbivore removal so instead of using the factor treatment in the model I'm using proportional herbivore damage. 

I have to use a package specific for beta distribution with 0's but we can talk about this in the context of a glmm using lme4 since that is the syntax I'm most familiar with.  My limited understanding leads me to:
Plant cover ~ herbivore damage + some covariates +(1|site)+(year|site/plot/subplot)
	Random variation between sites and, to account for repeated measures, subplots nested within plot nested within site sampled at a yearly interval for 	3 years.

As an additional curiosity, is there any problem with excluding the treatment factor and using proportional herbivore damage instead? Also, since site is included in the second random term, is the first term still necessary.  There is definitely variation between sites.  

Thank you for any assistance you're able to provide,
James