ARRY-380 + Trastuzuamab for Breast w/ Brain Mets

If a patient participates in this research study, the patient will receive ARRY-380 and a drug-dosing diary to record when the patient took ARRY-380 for each study treatment cycle. Each study treatment cycle will last for 3 weeks (21 days) during which time the patient will be taking ARRY-380 by mouth every day. At the time the patient enters the study, the patient will be assigned to either Arm A or Arm B. The difference between the two study arms includes ARRY-380 administered twice-daily (morning and evenings - Arm A) or once-daily (morning - Arm B). The patient will also be given Trastuzumab by intravenous infusion (by vein) on day 1 of each cycle (same dose and schedule for both study arms). The dose of trastuzumab will be the same for everyone on study, and will be the standard approved dose for this medication. In the first portion of the study, the investigators will examine the effects of different dose of ARRY-380 when given in combination with trastuzumab. Initially, 3 participants will be treated with a low dose of the ARRY-380 in combination with standard dose of trastuzumab. If this dose does not cause intolerable side effects, more participants may receive the drug combination at the same dose. The patient will be informed of the assigned dose when the patient enters the study. The patient will be asked to take ARRY-380 for as long as the study treatment is of possible benefit to the patient. After the patient is finished taking ARRY-380, the study doctor will ask the patient to visit the office for follow-up exams for at least one more visit within 4 weeks of the patient's last study treatment. At the start of each cycle the patient will have: * A medical history, which includes questions about health, current medications, and any allergies. * Performance status, which evaluates the ability to carry on with usual activities. * Physical examination, the doctor will examine the patient body, including measuring height, weight, and vital signs (blood pressure, body temperature, pulse rate and breathing rate). * A neurological examination to asses any neurological symptoms(for example, difficulties with balance) * Blood tests will be drawn at the beginning of each study treatment cycle for tests to monitor the function of liver and kidneys and to check blood cell counts. In addition, blood tests will be drawn on days 4, 8, and 15 of the first cycle of study treatment to monitor liver function. Periodically the patient will undergo: * The patient will have a brain MRI every two cycles. If the brain scans are stable or improved after the patient has been on the study for 6 months or longer, the frequency of your body scans will be decreased to once every 4 cycles. The patient will also have CT or MRI scans of the body at the end of cycle 2, cycle 4 and every 4 cycles thereafter. The research doctor may ask the patient to have a bone scan at the same time points if this is clinically indicated. * Electrocardiogram (EKG), which shows the electrical activity of the heart. It will be performed on Day 1 of cycle 2. * Echocardiogram (ECHO) (ultrasound of the heart) or MUGA scan (test of heart function using a small amount of a radioactive substance). This will be performed every 3-4 months. Additional research procedures to be performed: * On Cycle 1, Day 15 blood for ("PK") pharmacokinetic (what the body does to the drug) sampling will be drawn before the morning dose of ARRY-380, after 2 hours and after six hours. * Blood tests for research, which will include about 2 tablespoons of blood collected before cycle 1 and after coming off study treatment. In general terms, scientists will study the genes, the RNA, and the proteins that are found in the blood samples. Scientists will also measure and characterize circulating tumor cells in the blood, if they are present. In addition, these specimens may be tested with new types of tests, as they become available. Results of the research tests on blood will not be reported back to the patient. * Archival Tumor Tissue Sample: A sample (or samples) of the patient's tumor tissue (from a past surgery and/or biopsy) will be collected and used to learn more about the development of metastatic breast cancer. In general terms, scientists will study the genes, the RNA, and the proteins that are found both in breast tumors and in normal tissue. In addition, these specimens may be tested with new types of tests, as they become available. Laboratory-based investigators conducting this research will not have access to patient identification information such as name or medical record number. Results of the research tests on tissue will not be reported back to the patient. After the final dose of the study drug: The patient will have a follow-up visit one month after coming off study treatment. During that visit, the patient will have a physical examination, functional assessment, assessment of any toxicities and current medications. If the patient continues to have ongoing side effects related to the study treatment, the investigators will continue to follow the patient until these side effects resolve. If the patient withdrew from the study for another reason other than tumor progression, the patient will continue to be followed until tumor progression. Planned Follow-up: The investigators would like to keep track of the patient's medical condition indefinitely. The investigators would like to do this either by seeing the patient in clinic or by contacting the patient and the patient's primary doctor periodically to see how the patient is doing. Keeping in touch with the patient and checking the patient's condition periodically helps the investigators look at the long-term effects of the research study.