R&D is divided into various levels of "technological maturity." The lower levels that involve basic scientific investigation are usually addressed by research funding to colleges and universities via supervision by DARPA. A bit higher on the maturity level there is development of proof of concept technologies funded and performed by and collaboration with Office of Naval Research (for the naval services). A bit beyond that are experiments that for the Marine Corps are conducted by the Marine Corps Warfighting Laboratory. When a technology reaches a TRL 6 (technology readiness level) it may be transitioned into an acquisition program for a system that will be fielded for operational use. There are programs such as SBIR, STTR, and CRADAs for maturing and transitioning technology into programs. The Army and Air Force have similar R&D agencies but I'm most familiar with MCWL, ONR, and DARPA.
There are science and engineering internships available with these agencies.
If you have a proposal you can submit a white paper to solicit funding but it is best to have identified a validated requirement for which your R&D proposal would provide a solution.
[This message has been edited by Ulysses90 (edited 11/11/2011 9:34p).]